Parameters
Default parameter values used in simulations.
Alri
Name 
Description 
Type 
Value 

base_inc_rate_ALRI_by_RSV 
baseline incidence rate of Alri caused by RSV in age groups 011, 1223, 2459 months, per child per year 
List 
[0.165623001012122, 0.0368943809605977, 0.011883807410198] 
base_inc_rate_ALRI_by_Rhinovirus 
baseline incidence of Alri caused by Rhinovirus in age groups 011, 1223, 2459 months, per child per year 
List 
[0.0243368081563306, 0.0564272209432261, 0.0181754025659935] 
base_inc_rate_ALRI_by_HMPV 
baseline incidence of Alri caused by HMPV in age groups 011, 1223, 2459 months, per child per year 
List 
[0.0316242920447732, 0.01106932885584, 0.00356546901880363] 
base_inc_rate_ALRI_by_Parainfluenza 
baseline incidence of Alri caused by Parainfluenza 14 in age groups 011, 1223, 2459 months, per child per year 
List 
[0.0400689053941642, 0.0125990679490263, 0.00405820325903094] 
base_inc_rate_ALRI_by_Strep_pneumoniae_PCV13 
baseline incidence of Alri caused by Streptoccocus pneumoniae PCV13 serotype in age groups 011, 1223, 2459 months, per child per year 
List 
[0.00839805492638728, 0.0086009815601405, 0.00277040583791159] 
base_inc_rate_ALRI_by_Strep_pneumoniae_non_PCV13 
baseline incidence of Alri caused by Streptoccocus pneumoniae non PCV13 serotype in age groups 011, 1223, 2459 months, per child per year 
List 
[0.00971808948465436, 0.0056295094957977, 0.00181328443302487] 
base_inc_rate_ALRI_by_Hib 
baseline incidence of Alri caused by Haemophilus influenzae type b in age groups 011, 1223, 2459 months, per child per year 
List 
[0.00456369209787862, 0.00223809928508262, 0.000720899502209533] 
base_inc_rate_ALRI_by_H.influenzae_non_type_b 
baseline incidence of Alri caused by Haemophilus influenzae nontype b in age groups 011, 1223, 2459 months, per child per year 
List 
[0.0178046628079453, 0.00771804577106646, 0.00248600917371134] 
base_inc_rate_ALRI_by_Enterobacteriaceae 
baseline incidence of Alri caused by Enterobacteriaceae in age groups 011, 1223, 2459 months, per child per year 
List 
[0.00577447898013911, 0.00776959582619209, 0.002502613624339] 
base_inc_rate_ALRI_by_other_Strepto_Enterococci 
baseline incidence of Alri caused by other streptococci and Enterococci including Streptococcus pyogenes and Enterococcus faecium in age groups 011, 1223, 2459 months, per child per year 
List 
[0.00739221008020393, 0.000441075977443103, 0.000142072094251877] 
base_inc_rate_ALRI_by_Staph_aureus 
baseline incidence of Alri caused by Staphylococcus aureus in age groups 011, 1223, 2459 months, per child per year 
List 
[0.0230583713892271, 0.00164959730828988, 0.000531340984878809] 
base_inc_rate_ALRI_by_Influenza 
baseline incidence of Alri caused by Influenza type A, B, and C in age groups 011, 1223, 2459 months, per child per year 
List 
[0.0156895896609387, 0.00577122651203705, 0.00185893197294524] 
base_inc_rate_ALRI_by_P.jirovecii 
baseline incidence of Alri caused by P. jirovecii in age groups 011, 1223, 2459 months, per child per year 
List 
[0.00532021183938121, 0.00406616141018573, 0.00130972462037058] 
base_inc_rate_ALRI_by_other_viral_pathogens 
baseline incidence of Alri caused by other viral pathogens in age groups 011, 1223, 2459 months, per child per year 
List 
[0.0289052989892286, 0.0340001707821008, 0.0109515723253317] 
base_inc_rate_ALRI_by_other_bacterial_pathogens 
baseline incidence of Alri caused by other viral pathogens in age groups 011, 1223, 2459 months, per child per year 
List 
[0.0340967151177136, 0.0275272316777052, 0.00886661630515269] 
base_inc_rate_ALRI_by_other_pathogens_NoS 
baseline incidence of Alri caused by other pathogens not otherwise specified in age groups 011, 1223, 2459 months, per child per year 
List 
[0.012096954443426, 0.0244908799021158, 0.00788859692140824] 
proportion_pneumonia_in_RSV_ALRI 
proportion of RSVattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.469523118748083, 0.493147834326293] 
proportion_pneumonia_in_Rhinovirus_ALRI 
proportion of Rhinovirusattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.233411098940226, 0.300943850285401] 
proportion_pneumonia_in_HMPV_ALRI 
proportion of HMPVattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.514096212711081, 0.607661832402657] 
proportion_pneumonia_in_Parainfluenza_ALRI 
proportion of Parainfluenzaattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.381306534835401, 0.586394378700289] 
proportion_pneumonia_in_Strep_pneumoniae_PCV13_ALRI 
proportion of S. pneumoniae PCV13typeattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.419837201436785, 1] 
proportion_pneumonia_in_Strep_pneumoniae_non_PCV13_ALRI 
proportion of S. pneumoniae non PCV13typeattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.584526531211357, 0.47010416567094] 
proportion_pneumonia_in_Hib_ALRI 
proportion of Hib ALRIattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.643816417750475, 0.591228432603006] 
proportion_pneumonia_in_H.influenzae_non_type_b_ALRI 
proportion of H.influenzae non typebattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.484067635967411, 0.685783925920651] 
proportion_pneumonia_in_Staph_aureus_ALRI 
proportion of S. aureusattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.314311461687961, 0.668460076932899] 
proportion_pneumonia_in_Enterobacteriaceae_ALRI 
proportion of Enterobacteriaceaeattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.542743088827561, 0.397386416381317] 
proportion_pneumonia_in_other_Strepto_Enterococci_ALRI 
proportion of other Streptococci and Enterococciattributed ALRI manifesting as pneumoniaby age, (based on PERCH CXR+ results) 
List 
[0.794939501527616, 1] 
proportion_pneumonia_in_Influenza_ALRI 
proportion of Influenzaattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.274661773216931, 0.477667070122735] 
proportion_pneumonia_in_P.jirovecii_ALRI 
proportion of P. jiroveciiattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.773174448993322, 0.650848699225084] 
proportion_pneumonia_in_other_viral_pathogens_ALRI 
proportion of other viral pathogensattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.264286065267648, 0.301616616612727] 
proportion_pneumonia_in_other_bacterial_pathogens_ALRI 
proportion of other bacterial pathogensattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.321708555070697, 0.424616377668989] 
proportion_pneumonia_in_other_pathogens_NoS_ALRI 
proportion of other pathogens NoSattributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results) 
List 
[0.323847892119005, 0.256639724815326] 
rr_ALRI_HIV/AIDS 
relative rate of acquiring Alri for children with HIV+/AIDS 
Real 
6.51 
rr_ALRI_incomplete_measles_immunisation 
relative rate of acquiring Alri for children with incomplete measles immunisation 
Real 
1.8 
rr_ALRI_low_birth_weight 
relative rate of acquiring Alri for infants with low birth weight 
Real 
3.6 
rr_ALRI_non_exclusive_breastfeeding 
relative rate of acquiring Alri for not exclusive breastfeeding upto 6 months 
Real 
2.7 
rr_ALRI_indoor_air_pollution 
relative rate of acquiring Alri for indoor air pollution 
Real 
1.57 
prob_viral_pneumonia_bacterial_coinfection 
probability of primary viral pneumonia having a bacterial coinfection 
Real 
0.3 
proportion_bacterial_coinfection_pathogen 
list of proportions of each bacterial pathogens in a viral/bacterial coinfection pneumonia,the current values used are the pathogen attributable fractions (AFs) from PERCH for all ages. The AFs were scaled to bacterial pathogens only causes  value assumed to be the proportions of bacterial pathogens causing co/secondary infection 
List 
[0.107, 0.072, 0.038, 0.141, 0.134, 0.117, 0.052, 0.338] 
max_alri_duration_in_days_without_treatment 
maximum duration in days of untreated ALRI episode, assuming an average of 7 days 
Real 
14.0 
overall_progression_to_severe_ALRI 
probability of progression to severe ALRI 
Real 
0.12 
prob_pulmonary_complications_in_pneumonia 
probability of pulmonary complications in (CXR+) pneumonia 
Real 
0.215 
prob_pleural_effusion_in_pulmonary_complicated_pneumonia 
probability of pleural effusion in pneumonia with pulmonary complications 
Real 
0.938 
prob_empyema_in_pulmonary_complicated_pneumonia 
probability of empyema in pneumonia with pulmonary complications 
Real 
0.315 
prob_lung_abscess_in_pulmonary_complicated_pneumonia 
probability of lung abscess in pneumonia with pulmonary complications 
Real 
0.049 
prob_pneumothorax_in_pulmonary_complicated_pneumonia 
probability of pneumothorax in pneumonia with pulmonary complications 
Real 
0.049 
prob_hypoxaemia_in_pneumonia 
probability of hypoxaemia in pneumonia cases 
Real 
0.479 
prob_hypoxaemia_in_other_alri 
probability of hypoxaemia in bronchiolitis and other alri cases 
Real 
0.273 
prob_bacteraemia_in_pneumonia 
probability of bacteraemia in pneumonia 
Real 
0.039 
prob_progression_to_sepsis_with_bacteraemia 
probability of progression to sepsis from bactereamia 
Real 
0.3 
proportion_hypoxaemia_with_SpO2<90% 
proportion of hypoxaemic children with SpO2 <90% 
Real 
0.3576 
scaler_on_risk_of_death 
Multiplicative scaler on the overall risk of death, for the purpose of calibration. 
Real 
0.75 
base_odds_death_ALRI_age<2mo 
baseline odds of death from ALRI for young infants aged 0 month and severe pneumonia (base group) 
Real 
0.041965 
or_death_ALRI_age<2mo_very_severe_pneumonia 
odds ratio of death from ALRI for young infants with very severe pneumonia 
Real 
3.994783 
or_death_ALRI_age<2mo_P.jirovecii 
odds ratio of death from ALRI for young infants with P. jirovecii infection 
Real 
5.460986 
or_death_ALRI_age<2mo_by_month_increase_in_age 
odds ratio of death from ALRI for young infants by 1 month increase in age (1 month olds) 
Real 
0.6033254 
base_odds_death_ALRI_age2_59mo 
baseline odds of death from ALRI for children aged 2 months, male, no SAM, and nonsevere pneumonia classification (base group) 
Real 
0.0244725 
or_death_ALRI_age2_59mo_female 
odds ratio of death from ALRI for children who are female 
Real 
1.327285 
or_death_ALRI_age2_59mo_very_severe_pneumonia 
odds ratio of death from ALRI for children with very severe pneumonia 
Real 
8.382832 
or_death_ALRI_age2_59mo_P.jirovecii 
odds ratio of death from ALRI for children with P. jirovecii infection 
Real 
13.74696 
or_death_ALRI_age2_59mo_by_month_increase_in_age 
odds ratio of death from ALRI by 1 month increase in age for 2 to 59 months olds 
Real 
0.9661072 
or_death_ALRI_age2_59mo_SAM 
odds ratio of death from ALRI for children with severe acute malnutrition 
Real 
7.216448 
or_death_ALRI_SpO2<90% 
odds ratio of death from ALRI for children with oxygen saturation < 90%, base group: SpO2 <=93% 
Real 
5.04 
or_death_ALRI_SpO2_90_92% 
odds ratio of death from ALRI for children with oxygen saturation between 09 to 92%, base group: SpO2 <=93% 
Real 
1.54 
or_death_ALRI_sepsis 
odds ratio of death from ALRI for children with complication of sepsis (compared to if not) 
Real 
151.9 
or_death_ALRI_pneumothorax 
odds ratio of death from ALRI for children with complication of pneumothorax (compared to if not) 
Real 
77.4 
prob_cough_in_pneumonia 
probability of cough in pneumonia 
Real 
1.0 
prob_difficult_breathing_in_pneumonia 
probability of difficulty breathing in pneumonia 
Real 
1.0 
prob_fever_in_pneumonia 
probability of fever in pneumonia 
Real 
0.82 
prob_chest_indrawing_in_pneumonia 
probability of chest indrawing in pneumonia 
Real 
0.74 
prob_tachypnoea_in_pneumonia 
probability of tachypnoea in pneumonia 
Real 
0.834 
prob_danger_signs_in_pneumonia 
probability of any danger sign in pneumonia, including: : unable to drink, convulsions, cyanosis, head nodding/bobbing, irritability, abnormally sleepy, lethargy, nasal flaring, grunting 
Real 
0.28 
prob_cough_in_other_alri 
probability of cough in bronchiolitis or other alri 
Real 
1.0 
prob_difficult_breathing_in_other_alri 
probability of difficulty breathing in bronchiolitis or other alri 
Real 
1.0 
prob_fever_in_other_alri 
probability of fever in bronchiolitis or other alri 
Real 
0.76 
prob_tachypnoea_in_other_alri 
probability of tachypnoea in bronchiolitis or other alri 
Real 
0.758 
prob_chest_indrawing_in_other_alri 
probability of chest wall indrawing in bronchiolitis or other alri 
Real 
0.33 
prob_danger_signs_in_other_alri 
probability of any danger signs in bronchiolitis or other alri 
Real 
0.3 
prob_danger_signs_in_sepsis 
probability of any danger signs in ALRI complicated by sepsis 
Real 
1.0 
prob_danger_signs_in_SpO2<90% 
probability of any danger signs in children with SpO2 <90% 
Real 
0.313 
prob_danger_signs_in_SpO2_9092% 
probability of any danger signs in children with SpO2 between 9092% 
Real 
0.133 
prob_chest_indrawing_in_SpO2<90% 
probability of chest indrawing in children with SpO2 <90% 
Real 
0.701 
prob_chest_indrawing_in_SpO2_9092% 
probability of chest indrawing in children with SpO2 between 9092% 
Real 
0.445 
prob_cyanosis_in_other_alri 
probability of cyanosis in bronchiolitis or other alri 
Real 
0.04 
prob_cyanosis_in_pneumonia 
probability of cyanosis in pneumonia 
Real 
0.06 
prob_cyanosis_in_SpO2<90% 
probability of cyanosis when SpO2 < 90% 
Real 
0.078 
rr_Strep_pneum_VT_ALRI_with_PCV13_age<2y 
relative rate of acquiring S. pneumoniae vaccinetype Alri for children under 2 years of age immunised wth PCV13 
Real 
0.18 
rr_Strep_pneum_VT_ALRI_with_PCV13_age2to5y 
relative rate of acquiring S. pneumoniae vaccinetype Alri for children aged 2 to 5 immunised wth PCV13 
Real 
0.32 
rr_all_strains_Strep_pneum_ALRI_with_PCV13 
relative rate of acquiring S. pneumoniae all types Alri for children immunised wth PCV13 
Real 
0.45 
effectiveness_Hib_vaccine_on_Hib_strains 
effectiveness of Hib vaccine against H. influenzae typb ALRI 
Real 
0.86 
rr_Hib_ALRI_with_Hib_vaccine 
relative rate of acquiring H. influenzae typeb Alri for children immunised wth Hib vaccine 
Real 
0.14 
days_between_treatment_and_cure 
number of days between any treatment being given in an HSI and the cure occurring. 
Integer 
28 
tf_1st_line_antibiotic_for_severe_pneumonia 
Risk of treatment failure for a person with danger_signs_pneumonia being treated with first lineintravenous antibiotics 
Real 
0.11 
rr_tf_1st_line_antibiotics_if_cyanosis 
Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has the symptom of cyanosis.having that symptom. 
Real 
1.55 
rr_tf_1st_line_antibiotics_if_SpO2<90% 
Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has oxygen saturation < 90%. 
Real 
1.28 
rr_tf_1st_line_antibiotics_if_abnormal_CXR 
Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has a disease_type of “pneumonia”. 
Real 
1.71 
rr_tf_1st_line_antibiotics_if_MAM 
Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has un_clinical_acute_malnutrition == “MAM”. 
Real 
1.48 
rr_tf_1st_line_antibiotics_if_SAM 
Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has un_clinical_acute_malnutrition == “SAM”. 
Real 
2.02 
rr_tf_1st_line_antibiotics_if_HIV/AIDS 
Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has HIV and is not currently being treated. 
Real 
1.8 
or_mortality_improved_oxygen_systems 
Odds Ratio for the effect of oxygen provision to a person that needs oxygen who receives it, compares to a patient who does not. N.B. The inverse of this is used to reflect the increase in odds of death for a patient that needs oxygen but does not receive it. 
Real 
0.52 
tf_3day_amoxicillin_for_fast_breathing_with_SpO2>=90% 
probability of treatment failure by day 6 or relapse by day 14 of 3day course amoxicillin for treating fastbreathing pneumonia 
Real 
0.101 
tf_3day_amoxicillin_for_chest_indrawing_with_SpO2>=90% 
probability of treatment failure by day 6 or relapse by day 14 of 3day course amoxicillin for treating chestindrawing pneumonia without hypoxaemia (SpO2>=90%) 
Real 
0.125 
tf_5day_amoxicillin_for_chest_indrawing_with_SpO2>=90% 
probability of treatment failure by day 6 or relapse by day 14 of 5day course amoxicillin for treating chestindrawing pneumonia without hypoxaemia (SpO2>=90%) 
Real 
0.108 
tf_7day_amoxicillin_for_fast_breathing_pneumonia_in_young_infants 
probability of treatment failure by day 6 or relapse by day 14 of 5day course amoxicillin for treating chestindrawing pneumonia without hypoxaemia (SpO2>=90%) 
Real 
0.054 
tf_oral_amoxicillin_only_for_severe_pneumonia_with_SpO2>=90% 
probability of treatment failure by day 2 for oral amoxicillin given to severe pneumonia (dangersigns) without hypoxaemia (SpO2>=93%) 
Real 
0.6 
tf_oral_amoxicillin_only_for_non_severe_pneumonia_with_SpO2<90% 
probability of treatment failure or relapsefor oral amoxicillin given to nonsevere pneumonia (fastbreathing or chestindrawing) with hypoxaemia (SpO2<90%) 
Real 
0.2826 
tf_oral_amoxicillin_only_for_severe_pneumonia_with_SpO2<90% 
probability of treatment failure or relapsefor oral amoxicillin given to severe pneumonia (dangersigns) with hypoxaemia (SpO2<90%) 
Real 
0.8 
tf_2nd_line_antibiotic_for_severe_pneumonia 
probability of treatment failure by end of IV therapy for 2nd line antibiotic either cloxacillin or ceftriaxone to treat severe pneumonia (dangersigns) 
Real 
0.235 
sensitivity_of_classification_of_fast_breathing_pneumonia_facility_level0 
sensitivity of correct classification and treatment decision by the HSA trained in iCCM, using paperbased tools, for fastbreathing pneumonia 
Real 
0.7 
sensitivity_of_classification_of_danger_signs_pneumonia_facility_level0 
sensitivity of correct classification and referral decision by the HSA trained in iCCM, using paperbased tools, for dangersigns pneumonia 
Real 
0.7 
sensitivity_of_classification_of_non_severe_pneumonia_facility_level1 
sensitivity of correct classification and treatment decision for nonsevere pneumonia at facility level 1a and 1b 
Real 
0.7 
sensitivity_of_classification_of_severe_pneumonia_facility_level1 
sensitivity of correct classification and referral decision for severe pneumonia at facility level 1a and 1b 
Real 
0.7 
sensitivity_of_classification_of_non_severe_pneumonia_facility_level2 
sensitivity of correct classification and treatment decision for nonsevere pneumonia at facility level 2 
Real 
0.7 
sensitivity_of_classification_of_severe_pneumonia_facility_level2 
sensitivity of correct classification and treatment decision for severe pneumonia at facility level 2 
Real 
0.7 
prob_iCCM_severe_pneumonia_treated_as_fast_breathing_pneumonia 
probability of misdiagnosis of iCCM severe pneumonia (with chestindrawing or danger signs) given treatment for nonsevere pneumonia (fastbreathing) at facility level O 
Real 
0.7 
prob_IMCI_severe_pneumonia_treated_as_non_severe_pneumonia 
probability of misdiagnosis of IMCI severe pneumonia (with danger signs) given treatment for nonsevere pneumonia ( fastbreathing or chestindrawing) at facility level 1a/1b/2 
Real 
0.7 
or_care_seeking_perceived_severe_illness 
The Odds Ratio for healthcare seeking for the symptom of chestindrawing 
Real 
2.4 
pulse_oximeter_and_oxygen_is_available 
Control the availability of the pulse oximeter and oxygen. “Default” does not override availability; “Yes” forces them to be available; “No” forces them to not be available 
Categorical 
Default 
prob_for_followup_if_treatment_failure 
The probability for scheduling a followup appointment following treatment failure 
Real 
0.3 
BladderCancer
Name 
Description 
Type 
Value 

init_prop_bladder_cancer_stage 
initial proportions in bladder cancer categories for person aged 1519 and no tobacco and no schisto_h 
List 
[5e05, 5e05, 5e05] 
init_prop_blood_urine_bladder_cancer_by_stage 
initial proportions of those with bladder cancer categories that have the symptom blood urine 
List 
[0.2, 0.5, 0.7] 
init_prop_pelvic_pain_bladder_cancer_by_stage 
initial proportions of those with bladder cancer categories that have pelvic pain 
List 
[0.0, 0.3, 0.5] 
init_prop_with_blood_urine_diagnosed_bladder_cancer_by_stage 
initial proportions of people that have symptom of blood urine that have been diagnosed 
List 
[0.7, 0.9, 0.9] 
init_prop_with_pelvic_pain_diagnosed_bladder_cancer_by_stage 
initial proportions of people that have symptom of pelvic pain that have been diagnosed 
List 
[0.0, 0.7, 0.9] 
init_prop_treatment_status_bladder_cancer 
initial proportions of people with bladder cancer that had initiated treatment 
List 
[0.05, 0.05, 0.05] 
init_prob_palliative_care 
initial probability of being under palliative care if in metastatic 
Real 
0.95 
r_tis_t1_bladder_cancer_none 
probability per 3 months of incident tis_t1 bladder cancer, amongst people with no bladder cancer(for person aged 1519 and no tobacco and no schisto_h) 
Real 
1e05 
rr_tis_t1_bladder_cancer_none_age3049 
rate ratio for tis_t1 bladder cancer for age 3049 
Real 
2.0 
rr_tis_t1_bladder_cancer_none_age5069 
rate ratio for tis_t1 bladder cancer for age 5069 
Real 
3.0 
rr_tis_t1_bladder_cancer_none_agege70 
rate ratio for tis_t1 bladder cancer for age 70+ 
Real 
3.0 
rr_tis_t1_bladder_cancer_none_tobacco 
rate ratio for tis_t1 bladder cancer for tobacco smokers 
Real 
3.5 
rr_tis_t1_bladder_cancer_none_schisto_h 
rate ratio for tis_t1 bladder cancer for schisto_h 
Real 
5.0 
r_t2p_bladder_cancer_tis_t1 
probability per 3 months of t2+ bladder cancer, amongst people with tis_t1 bladder cancer 
Real 
0.05 
rr_t2p_bladder_cancer_undergone_curative_treatment 
rate ratio for t2+ bladder cancer for people with tis_t1 bladder cancer if had curative treatment at tis_t1 bladder cancer stage 
Real 
0.1 
r_metastatic_t2p_bladder_cancer 
probability per 3 months of metastatic bladder cancer amongst people with t2+ bladder cancer 
Real 
0.05 
rr_metastatic_undergone_curative_treatment 
rate ratio for metastatic bladder cancer for people with t2+ bladder cancer if had curative treatment at t2+ bladder cancer stage 
Real 
0.2 
rate_palliative_care_metastatic 
prob palliative care this 3 month period if metastatic bladder cancer 
Real 
0.2 
r_death_bladder_cancer 
probability per 3 months of death from bladder cancer amongst people with metastatic bladder cancer 
Real 
0.05 
r_blood_urine_tis_t1_bladder_cancer 
probability per 3 months of blood_urine in a person with tis_t1 bladder cancer 
Real 
0.01 
rr_blood_urine_t2p_bladder_cancer 
rate ratio for blood_urine if have t2p bladder cancer 
Real 
3.0 
rr_blood_urine_metastatic_bladder_cancer 
rate ratio for blood_urine if have metastatic bladder cancer 
Real 
3.0 
r_pelvic_pain_tis_t1_bladder_cancer 
probability per 3 months of pelvic_pain in a person with tis_t1 bladder cancer 
Real 
0.0003 
rr_pelvic_pain_t2p_bladder_cancer 
rate ratio for pelvic_pain if have t2p bladder cancer 
Real 
200.0 
rr_pelvic_pain_metastatic_bladder_cancer 
rate ratio for pelvic_pain if have metastatic bladder cancer 
Real 
300.0 
rp_bladder_cancer_age3049 
relative prevalence at baseline of bladder cancer/cancer age 3049 
Real 
2.0 
rp_bladder_cancer_age5069 
relative prevalence at baseline of bladder cancer/cancer age 5069 
Real 
3.0 
rp_bladder_cancer_agege70 
relative prevalence at baseline of bladder cancer/cancer age 70+ 
Real 
3.0 
rp_bladder_cancer_tobacco 
relative prevalence at baseline of bladder cancer if tobacco 
Real 
3.5 
rp_bladder_cancer_schisto_h 
relative prevalence at baseline of bladder cancer if schisto_h 
Real 
5.0 
sensitivity_of_cystoscopy_for_bladder_cancer_blood_urine 
sensitivity of cystoscopy_for diagnosis of bladder cancer given blood urine 
Real 
1.0 
sensitivity_of_cystoscopy_for_bladder_cancer_pelvic_pain 
sensitivity of cystoscopy_for diagnosis of bladder cancer given pelvic pain 
Real 
1.0 
BreastCancer
Name 
Description 
Type 
Value 

init_prop_breast_cancer_stage 
initial proportions in cancer categories for woman aged 1529 
List 
[5e05, 5e05, 5e05, 1.5e05] 
init_prop_breast_lump_discernible_breast_cancer_by_stage 
initial proportions of those with cancer categories that have the symptom breast_lump_discernible 
List 
[0.5, 0.8, 0.9, 0.98] 
init_prop_with_breast_lump_discernible_diagnosed_breast_cancer_by_stage 
initial proportions of people that have breast_lump_discernible that have been diagnosed 
List 
[0.9, 0.9, 0.9, 0.9] 
init_prop_treatment_status_breast_cancer 
initial proportions of people with breast cancer previously treated 
List 
[0.1, 0.1, 0.1, 0.1] 
init_prob_palliative_care 
initial probability of being under palliative care if in stage 4 
Real 
0.8 
r_stage1_none 
probabilty per 3 months of incident stage 1 breast, amongst people with no breast cancer 
Real 
2e06 
rr_stage1_none_age3049 
rate ratio for stage1 breast cancer for age 3049 
Real 
20.0 
rr_stage1_none_agege50 
rate ratio for stage1 breast cancer for age 50+ 
Real 
20.0 
r_stage2_stage1 
probabilty per 3 months of stage 2 breast cancer amongst people with stage 1 
Real 
0.15 
rr_stage2_undergone_curative_treatment 
rate ratio for stage 2 breast cancer for people with stage 1 breast cancer if had curative treatment at stage 1 
Real 
0.05 
r_stage3_stage2 
probabilty per 3 months of stage 3 breast cancer amongst people with stage 2 
Real 
0.15 
rr_stage3_undergone_curative_treatment 
rate ratio for stage 3 breast cancer for people with stage 2 breast cancer if had curative treatment at stage 2 
Real 
0.05 
r_stage4_stage3 
probabilty per 3 months of stage 4 breast cancer amongst people with stage 3 
Real 
0.15 
rr_stage4_undergone_curative_treatment 
rate ratio for stage 4 breast cancer for people with stage 3 breast cancer if had curative treatment at stage 3 
Real 
0.5 
r_death_breast_cancer 
probabilty per 3 months of death from breast cancer amongst people with stage 4 breast cancer 
Real 
0.1 
r_breast_lump_discernible_stage1 
rate ratio for breast_lump_discernible if have stage 1 breast cancer 
Real 
0.05 
rr_breast_lump_discernible_stage2 
rate ratio for breast_lump_discernible if have stage 2 breast cancer 
Real 
2.0 
rr_breast_lump_discernible_stage3 
rate ratio for breast_lump_discernible if have stage 3 breast cancer 
Real 
4.0 
rr_breast_lump_discernible_stage4 
rate ratio for breast_lump_discernible if have stage 4 breast cancer 
Real 
10.0 
rp_breast_cancer_age3049 
relative prevalence at baseline of breast cancer if age3049 
Real 
20.0 
rp_breast_cancer_agege50 
relative prevalence at baseline of breast cancer if agege50 
Real 
20.0 
sensitivity_of_biopsy_for_stage1_breast_cancer 
sensitivity of biopsy_for diagnosis of stage 1 breast cancer 
Real 
0.8 
sensitivity_of_biopsy_for_stage2_breast_cancer 
sensitivity of biopsy_for diagnosis of stage 2 breast cancer 
Real 
0.95 
sensitivity_of_biopsy_for_stage3_breast_cancer 
sensitivity of biopsy_for diagnosis of stage 3 breast cancer 
Real 
0.95 
sensitivity_of_biopsy_for_stage4_breast_cancer 
sensitivity of biopsy_for diagnosis of stage 4 breast cancer 
Real 
0.95 
CardioMetabolicDisorders
Name 
Description 
Type 
Value 

diabetes_onset 
all the parameters that specify the linear models for onset of diabetes 
Series 

hypertension_onset 
all the parameters that specify the linear models for onset of hypertension 
Series 

chronic_kidney_disease_onset 
all the parameters that specify the linear models for onset of chronic_kidney_disease 
Series 

chronic_lower_back_pain_onset 
all the parameters that specify the linear models for onset of chronic_lower_back_pain 
Series 

chronic_ischemic_hd_onset 
all the parameters that specify the linear models for onset of chronic_ischemic_hd 
Series 

diabetes_removal 
all the parameters that specify the linear models for removal of diabetes 
Series 

hypertension_removal 
all the parameters that specify the linear models for removal of hypertension 
Series 

chronic_kidney_disease_removal 
all the parameters that specify the linear models for removal of chronic_kidney_disease 
Series 

chronic_lower_back_pain_removal 
all the parameters that specify the linear models for removal of chronic_lower_back_pain 
Series 

chronic_ischemic_hd_removal 
all the parameters that specify the linear models for removal of chronic_ischemic_hd 
Series 

diabetes_hsi 
all the parameters that specify diagnostic tests and treatments for diabetes 
Series 

hypertension_hsi 
all the parameters that specify diagnostic tests and treatments for hypertension 
Series 

chronic_kidney_disease_hsi 
all the parameters that specify diagnostic tests and treatments for chronic_kidney_disease 
Series 

chronic_lower_back_pain_hsi 
all the parameters that specify diagnostic tests and treatments for chronic_lower_back_pain 
Series 

chronic_ischemic_hd_hsi 
all the parameters that specify diagnostic tests and treatments for chronic_ischemic_hd 
Series 

ever_stroke_onset 
all the parameters that specify the linear models for onset of ever_stroke 
Series 

ever_heart_attack_onset 
all the parameters that specify the linear models for onset of ever_heart_attack 
Series 

diabetes_death 
all the parameters that specify the linear models for death from diabetes 
Series 

hypertension_death 
all the parameters that specify the linear models for death from hypertension 
Series 

chronic_kidney_disease_death 
all the parameters that specify the linear models for death from chronic_kidney_disease 
Series 

chronic_lower_back_pain_death 
all the parameters that specify the linear models for death from chronic_lower_back_pain 
Series 

chronic_ischemic_hd_death 
all the parameters that specify the linear models for death from chronic_ischemic_hd 
Series 

ever_stroke_death 
all the parameters that specify the linear models for death from ever_stroke 
Series 

ever_heart_attack_death 
all the parameters that specify the linear models for death from ever_heart_attack 
Series 

ever_stroke_hsi 
all the parameters that specify diagnostic tests and treatments for ever_stroke 
Series 

ever_heart_attack_hsi 
all the parameters that specify diagnostic tests and treatments for ever_heart_attack 
Series 

diabetes_initial_prev 
initial prevalence of condition 
Series 

hypertension_initial_prev 
initial prevalence of condition 
Series 

chronic_kidney_disease_initial_prev 
initial prevalence of condition 
Series 

chronic_lower_back_pain_initial_prev 
initial prevalence of condition 
Series 

chronic_ischemic_hd_initial_prev 
initial prevalence of condition 
Series 

interval_between_polls 
months between the main polling event 
Integer 
3 
pr_bmi_reduction 
probability of an individual having a reduction in BMI following weight loss treatment 
Real 
0.1 
prob_care_provided_given_seek_emergency_care 
The probability that correct care is fully provided to persons that have sought emergency care for a Cardiometabolic disorder. 
Real 
0.5 
diabetes_onset
value 

1.15 
0 
0 
0 
0 
1 
1 
1.6 
2.21538 
Only first 10 rows of 67 are shown.
hypertension_onset
value 

0.95 
0 
0 
0 
0 
0.337838 
1.00338 
1.00338 
1 
Only first 10 rows of 67 are shown.
chronic_kidney_disease_onset
value 

1.25 
0 
0 
0 
0 
0.515464 
0.515464 
0.515464 
1 
Only first 10 rows of 67 are shown.
chronic_lower_back_pain_onset
value 

1 
0 
0 
0 
0 
0.69 
1 
1.44615 
2.21538 
Only first 10 rows of 67 are shown.
chronic_ischemic_hd_onset
value 

2.3 
0 
0 
0 
0 
0.140136 
1 
1 
1 
Only first 10 rows of 67 are shown.
diabetes_removal
value 

0 
0 
0 
0 
0 
0 
0 
0 
0 
Only first 10 rows of 67 are shown.
hypertension_removal
value 

0 
0 
0 
0 
0 
0 
0 
0 
0 
Only first 10 rows of 67 are shown.
chronic_kidney_disease_removal
value 

0 
0 
0 
0 
0 
0 
0 
0 
0 
Only first 10 rows of 67 are shown.
chronic_lower_back_pain_removal
value 

0.8 
0 
0 
0 
0 
1 
1 
1 
1 
Only first 10 rows of 67 are shown.
chronic_ischemic_hd_removal
value 

0 
0 
0 
0 
0 
0 
0 
0 
0 
Only first 10 rows of 67 are shown.
diabetes_hsi
value 

216 
1 
233 
0.1 
0.42 
0.3846 
0.8 
hypertension_hsi
value 

1 
221 
0.05 
0 
0.3797 
0.8 
chronic_kidney_disease_hsi
value 

47 
1 
2064 
0 
0 
0.02 
0.8 
chronic_lower_back_pain_hsi
value 

1 
226 
0 
0 
0 
0.1 
chronic_ischemic_hd_hsi
value 

1 
226 
0 
0 
0.05 
0.8 
ever_stroke_onset
value 

0.9 
0 
0 
0 
0 
0.15 
0.15 
0.15 
0.17 
Only first 10 rows of 67 are shown.
ever_heart_attack_onset
value 

1.5 
0 
0 
0 
0 
0.05 
0.05 
0.05 
0.05 
Only first 10 rows of 67 are shown.
diabetes_death
value 

3.2 
0 
0 
0 
0 
0.2 
0.2 
0.25 
0.25 
Only first 10 rows of 67 are shown.
hypertension_death
value 

0 
0 
0 
0 
0 
0 
0 
0 
0 
Only first 10 rows of 67 are shown.
chronic_kidney_disease_death
value 

2.2 
0 
0 
0 
0 
0.25 
0.2 
0.2 
0.3 
Only first 10 rows of 67 are shown.
chronic_lower_back_pain_death
value 

0 
0 
0 
0 
0 
0 
0 
0 
0 
Only first 10 rows of 67 are shown.
chronic_ischemic_hd_death
value 

1.4 
0 
0 
0 
0 
0.673277 
0.673277 
0.615122 
0.641215 
Only first 10 rows of 67 are shown.
ever_stroke_death
value 

1 
0 
0 
0 
0 
0.2 
0.2 
0.35 
0.35 
Only first 10 rows of 67 are shown.
ever_heart_attack_death
value 

1.8 
0 
0 
0 
0 
0.1 
0.1 
0.15 
0.15 
Only first 10 rows of 67 are shown.
ever_stroke_hsi
value 

1 
226 
0 
234 
0.59 
ever_heart_attack_hsi
value 

1 
226 
0 
225 
0.481 
diabetes_initial_prev
value 

0 
0 
0 
0.00168696 
0.00168696 
0.0100913 
0.0100913 
0.0203044 
0.0203044 
Only first 10 rows of 42 are shown.
hypertension_initial_prev
value 

0 
0 
0 
0.0468696 
0.0468696 
0.101778 
0.101778 
0.128891 
0.128891 
Only first 10 rows of 42 are shown.
chronic_kidney_disease_initial_prev
value 

0 
0 
0 
0.0003 
0.0003 
0.0009 
0.0009 
0.0033 
0.0033 
Only first 10 rows of 42 are shown.
chronic_lower_back_pain_initial_prev
value 

0.0053 
0.0229 
0.0341 
0.0411 
0.0534 
0.0657 
0.0819 
0.0973 
0.1095 
Only first 10 rows of 42 are shown.
chronic_ischemic_hd_initial_prev
value 

0 
0 
0.0001 
0.0005 
0.0015 
0.0033 
0.0065 
0.0125 
0.0225 
Only first 10 rows of 42 are shown.
CareOfWomenDuringPregnancy
Name 
Description 
Type 
Value 

prob_seek_anc2 
Probability a woman who is not predicted to attended four or more ANC visits will attend ANC2 
List 
[0.98, 0.98] 
prob_seek_anc3 
Probability a woman who is not predicted to attended four or more ANC visits will attend ANC3 
List 
[0.55, 0.55] 
prob_seek_anc5 
Probability a woman who is predicted to attend four or more ANC visits will attend ANC5 
List 
[0.125, 0.125] 
prob_seek_anc6 
Probability a woman who is predicted to attend four or more ANC visits will attend ANC6 
List 
[0.0625, 0.0625] 
prob_seek_anc7 
Probability a woman who is predicted to attend four or more ANC visits will attend ANC7 
List 
[0.03125, 0.03125] 
prob_seek_anc8 
Probability a woman who is predicted to attend four or more ANC visits will attend ANC8 
List 
[0.03125, 0.03125] 
effect_of_ifa_for_resolving_anaemia 
treatment effectiveness of starting iron and folic acid on resolving anaemia 
List 
[0.7, 0.7] 
treatment_effect_blood_transfusion_anaemia 
treatment effectiveness of blood transfusion for anaemia in pregnancy 
List 
[0.9, 0.9] 
prob_intervention_delivered_urine_ds 
probability a woman will receive the intervention “urine dipstick” given that the HSI has ran and the consumables are available (proxy for clinical quality) 
List 
[0.53, 0.53] 
prob_intervention_delivered_bp 
probability a woman will receive the intervention “blood pressure measurement” given that the HSI has ran and the consumables are available (proxy for clinical quality) 
List 
[0.7, 0.69] 
prob_adherent_ifa 
probability a woman who is given iron and folic acid will adhere to the treatment for their pregnancy 
List 
[0.37, 0.34] 
prob_intervention_delivered_syph_test 
probability a woman will receive the intervention “Syphilis test” given that the HSI has ran and the consumables are available (proxy for clinical quality) 
List 
[0.43, 0.14] 
prob_intervention_delivered_gdm_test 
probability a woman will receive the intervention “GDM screening” given that the HSI has ran and the consumables are available (proxy for clinical quality) 
List 
[0.48, 0.48] 
prob_delivery_modes_ec 
probabilities that a woman admitted with eclampsia will deliver normally, via caesarean or via assisted vaginal delivery 
List 
[[0, 0, 1], [0, 0, 1]] 
prob_delivery_modes_spe 
probabilities that a woman admitted with severe preeclampsia will deliver normally, via caesarean or via assisted vaginal delivery 
List 
[[0.05, 0.05, 0.9], [0.05, 0.05, 0.9]] 
sensitivity_bp_monitoring 
sensitivity of blood pressure monitoring to detect hypertension 
List 
[0.74, 0.74] 
specificity_bp_monitoring 
specificity of blood pressure monitoring to detect hypertension 
List 
[0.79, 0.79] 
sensitivity_urine_protein_1_plus 
sensitivity of a urine dipstick test to detect proteinuria at 1+ 
List 
[0.541, 0.541] 
specificity_urine_protein_1_plus 
specificity of a urine dipstick test to detect proteinuria at 1+ 
List 
[0.841, 0.841] 
sensitivity_poc_hb_test 
sensitivity of a point of care Hb test to detect anaemia 
List 
[0.851, 0.851] 
specificity_poc_hb_test 
specificity of a point of care Hb test to detect anaemia 
List 
[0.801, 0.801] 
sensitivity_fbc_hb_test 
sensitivity of a Full Blood Count test to detect anaemia 
List 
[1.0, 1.0] 
specificity_fbc_hb_test 
specificity of a Full Blood Count test to detect anaemia 
List 
[1.0, 1.0] 
sensitivity_blood_test_glucose 
sensitivity of a blood test to detect raised blood glucose 
List 
[1.0, 1.0] 
specificity_blood_test_glucose 
specificity of a blood test to detect raised blood glucose 
List 
[1.0, 1.0] 
sensitivity_blood_test_syphilis 
sensitivity of a blood test to detect syphilis 
List 
[0.82, 0.82] 
specificity_blood_test_syphilis 
specificity of a blood test to detect syphilis 
List 
[0.96, 0.96] 
Contraception
Name 
Description 
Type 
Value 

Method_Use_In_2010 
Proportion of women using each method in 2010, by age. 
Dataframe 

Pregnancy_NotUsing_In_2010 
Probability per year of a women not on contraceptive becoming pregnant, by age. 
Dataframe 

Pregnancy_NotUsing_HIVeffect 
Relative probability of becoming pregnant whilst not using a a contraceptive for HIVpositive women compared to HIVnegative women. 
Dataframe 

Failure_ByMethod 
Probability per month of a women on a contraceptive becoming pregnant, by method. 
Dataframe 

rr_fail_under25 
The relative risk of becoming pregnant whilst using a contraceptive for woman younger than 25 years compared to older women. 
Real 
2.2 
Initiation_ByMethod 
Probability per month of a women who is not using any contraceptive method of starting use of a method, by method. 
Dataframe 

Interventions_Pop 
Pop (population scale contraception intervention) intervention multiplier. 
Dataframe 

Interventions_PPFP 
PPFP (postpartum family planning) intervention multiplier. 
Dataframe 

Initiation_ByAge 
The effect of age on the probability of starting use of contraceptive (add one for multiplicative effect). 
Dataframe 

Initiation_AfterBirth 
The probability of a woman starting a contraceptive immidiately after birth, by method. 
Dataframe 

Discontinuation_ByMethod 
The probability per month of discontinuing use of a method, by method. 
Dataframe 

Discontinuation_ByAge 
The effect of age on the probability of discontinuing use of contraceptive (add one for multiplicative effect). 
Dataframe 

Prob_Switch_From 
The probability per month that a women switches from one form of contraceptive to another, conditional that she will not discontinue use of the method. 
Dataframe 

Prob_Switch_From_And_To 
The probability of switching to a new method, by method, conditional that the woman will switch to a new method. 
Dataframe 

days_between_appts_for_maintenance 
The number of days between successive family planning appointments for women that are maintaining the use of a method (for each method insorted(self.states_that_may_require_HSI_to_maintain_on), i.e.[IUD, implant, injections, other_modern, pill]). 
List 
[4383, 1461, 91, 91, 91, 91] 
age_specific_fertility_rates 
Data table from official source (WPP) for agespecific fertility rates and calendar period. 
Dataframe 

scaling_factor_on_monthly_risk_of_pregnancy 
Scaling factor (by agegroup: 1519, 2024, …, 4549) on the monthly risk of pregnancy and contraceptive failure rate. This value is found through calibration so that, at the beginning of the simulation, the agespecific monthly probability of a woman having a live birth matches the WPP agespecific fertility rate value for the same year. 
List 
[1.227, 0.7191, 0.6632, 0.84945, 0.86135, 0.645, 0.941] 
max_number_of_runs_of_hsi_if_consumable_not_available 
The maximum number of time an HSI can run (repeats occur if the consumables are not available). 
Integer 
1000 
max_days_delay_between_decision_to_change_method_and_hsi_scheduled 
The maximum delay (in days) between the decision for a contraceptive to change and the topen date of the HSI that is scheduled to effect the change (when using the healthsystem). 
Integer 
7 
use_interventions 
if True: FP interventions (pop & ppfp) are simulated from the date ‘interventions_start_date’, if False: FP interventions (pop & ppfp) are not simulated. 
Boolean 
False 
interventions_start_date 
The date since which the FP interventions (pop & ppfp) are implemented, if at all (ie, if use_interventions==True 
Date 
20230101 00:00:00 
Method_Use_In_2010
age 
not_using 
pill 
IUD 
injections 
implant 
male_condom 
female_sterilization 
other_modern 
periodic_abstinence 
withdrawal 
other_traditional 

16 
0.956447 
0 
0.000853971 
0.0187874 
0 
0.0204953 
0 
0 
0.00256191 
0 
0.000853971 
17 
0.917373 
0.00105932 
0 
0.0413136 
0 
0.0275424 
0 
0 
0.00317797 
0.00741525 
0.00105932 
18 
0.843715 
0.00679502 
0 
0.103058 
0 
0.0396376 
0 
0 
0 
0.00566251 
0 
19 
0.738693 
0.0188442 
0 
0.182161 
0 
0.0376884 
0 
0 
0.00125628 
0.0138191 
0.00251256 
20 
0.693305 
0.0107991 
0 
0.218143 
0 
0.0410367 
0.00431965 
0 
0.00215983 
0.0215983 
0.00323974 
21 
0.644362 
0.0173482 
0.00123916 
0.272615 
0 
0.0371747 
0.00123916 
0 
0.00123916 
0.00743494 
0.00619579 
22 
0.634744 
0.018931 
0 
0.26392 
0 
0.0356347 
0.00445434 
0 
0.00556793 
0.0155902 
0.00668151 
23 
0.642616 
0.00676437 
0.00225479 
0.264938 
0 
0.0394588 
0.00338219 
0 
0.00789177 
0.0124014 
0.00676437 
24 
0.588101 
0.020595 
0.00114416 
0.286041 
0 
0.0297483 
0.0125858 
0 
0.00800915 
0.0228833 
0.00915332 
Only first 10 rows of 35 are shown.
Pregnancy_NotUsing_In_2010
age 
AnnualProb 

16 
0.0780862 
17 
0.148498 
18 
0.298088 
19 
0.402345 
20 
0.532862 
21 
0.552413 
22 
0.586474 
23 
0.569371 
24 
0.598742 
Only first 10 rows of 35 are shown.
Pregnancy_NotUsing_HIVeffect
RR_pregnancy 


16 
1.4 
17 
1.4 
18 
1.4 
19 
1.4 
20 
0.9 
21 
0.9 
22 
0.9 
23 
0.9 
24 
0.9 
Only first 10 rows of 35 are shown.
Failure_ByMethod
pill 
IUD 
injections 
implant 
male_condom 
female_sterilization 
other_modern 
periodic_abstinence 
withdrawal 
other_traditional 

0.00192848 
0 
0.000530667 
9.50789e05 
0.00117109 
0 
0 
0.000552797 
0.00358032 
0.004923 
Initiation_ByMethod
not_using 
pill 
IUD 
injections 
implant 
male_condom 
female_sterilization 
other_modern 
periodic_abstinence 
withdrawal 
other_traditional 

0.993934 
0.000397942 
1.84759e05 
0.00382829 
0.000117488 
0.000793041 
0.000274295 
2.5582e05 
9.2853e05 
0.000358621 
0.000159177 
Interventions_Pop
pill 
IUD 
injections 
implant 
male_condom 
female_sterilization 
other_modern 
periodic_abstinence 
withdrawal 
other_traditional 

2.5 
11 
1.6 
8 
2.6 
2 
5 
1 
1 
1 
Interventions_PPFP
pill 
IUD 
injections 
implant 
male_condom 
female_sterilization 
other_modern 
periodic_abstinence 
withdrawal 
other_traditional 

2.5 
11 
1.6 
8 
2.6 
2 
5 
1 
1 
1 
Initiation_ByAge
age 
r_init1_age 

16 
0.224538 
17 
0.147192 
18 
0.089718 
19 
0.0469456 
20 
0.0151724 
21 
0.00829227 
22 
0.0254293 
23 
0.0377144 
24 
0.0462588 
Only first 10 rows of 35 are shown.
Initiation_AfterBirth
not_using 
pill 
IUD 
injections 
implant 
male_condom 
female_sterilization 
other_modern 
periodic_abstinence 
withdrawal 
other_traditional 

0.99654 
0.000224019 
5.84398e06 
0.00180189 
5.06478e05 
0.000210383 
0.000718809 
1.1688e05 
0.000105192 
0.000181163 
0.000149995 
Discontinuation_ByMethod
pill 
IUD 
injections 
implant 
male_condom 
female_sterilization 
other_modern 
periodic_abstinence 
withdrawal 
other_traditional 

0.0496232 
0.0111009 
0.0333511 
0.00627062 
0.0503725 
0 
0.0332874 
0.0422692 
0.0423377 
0.0497931 
Discontinuation_ByAge
age 
r_discont_age 

16 
0.628712 
17 
0.438627 
18 
0.29471 
19 
0.185198 
20 
0.101633 
21 
0.037841 
22 
0.0107489 
23 
0.0475587 
24 
0.0751794 
Only first 10 rows of 35 are shown.
Prob_Switch_From
pill 
IUD 
injections 
implant 
male_condom 
female_sterilization 
other_modern 
periodic_abstinence 
withdrawal 
other_traditional 

0.0109093 
0.00145124 
0.0030322 
0.000862686 
0.0114341 
0 
0.00265503 
0.00751371 
0.0137878 
0.027214 
Prob_Switch_From_And_To
switchfrom 
pill 
IUD 
injections 
implant 
male_condom 
female_sterilization 
other_modern 
periodic_abstinence 
withdrawal 
other_traditional 

pill 
0 
0 
0.540323 
0.217742 
0.104839 
0.0564516 
0.0241935 
0.00806452 
0.0403226 
0.00806452 
IUD 
0.125 
0 
0.375 
0.25 
0.125 
0.125 
0 
0 
0 
0 
injections 
0.262806 
0.0267261 
0 
0.447661 
0.106904 
0.0757238 
0.00890869 
0.00890869 
0.0445434 
0.0178174 
implant 
0.205882 
0.0294118 
0.632353 
0 
0.102941 
0.0294118 
0 
0 
0 
0 
male_condom 
0.0829268 
0.00487805 
0.595122 
0.22439 
0 
0.0292683 
0.00487805 
0.0097561 
0.0487805 
0 
other_modern 
0 
0 
1 
0 
0 
0 
0 
0 
0 
0 
periodic_abstinence 
0 
0 
0.333333 
0.666667 
0 
0 
0 
0 
0 
0 
withdrawal 
0.037037 
0.0185185 
0.518519 
0.296296 
0.111111 
0.0185185 
0 
0 
0 
0 
other_traditional 
0 
0 
0.73913 
0.144928 
0.057971 
0.057971 
0 
0 
0 
0 
age_specific_fertility_rates
Variant 
Period 
Age_Grp 
asfr 

WPP_Estimates 
19551959 
1519 
0.183883 
WPP_Estimates 
19601964 
1519 
0.186647 
WPP_Estimates 
19651969 
1519 
0.191979 
WPP_Estimates 
19701974 
1519 
0.197259 
WPP_Estimates 
19751979 
1519 
0.202538 
WPP_Estimates 
19801984 
1519 
0.202538 
WPP_Estimates 
19851989 
1519 
0.193211 
WPP_Estimates 
19901994 
1519 
0.159343 
WPP_Estimates 
19951999 
1519 
0.160904 
Only first 10 rows of 434 are shown.
Copd
Name 
Description 
Type 
Value 

prob_mod_exacerb 
probability of moderate exacerbation given lung function, for each lung function category. 
List 
[0, 0, 0, 0.01, 0.05, 0.2, 0.3] 
prob_sev_exacerb 
probability of severe exacerbation given lung function, for each lung function category. 
List 
[0, 0, 0, 0.0, 0.0, 0.05, 0.1] 
prob_progress_to_next_cat 
probability of changing from a lower lung function category to a higher lung function category 
Real 
0.015 
prob_will_die_sev_exacerbation_ge80 
probability that a person equal to or greater than 80 years will die of severe exacerbation 
Real 
0.95 
prob_will_die_sev_exacerbation_7079 
probability that a person between 70 to 79 years will die of severe exacerbation 
Real 
0.7 
prob_will_die_sev_exacerbation_6069 
probability that a person between 60 to 99 years will die of severe exacerbation 
Real 
0.5 
prob_will_die_sev_exacerbation_5059 
probability that a person between 50 to 59 years will die of severe exacerbation 
Real 
0.05 
prob_will_die_sev_exacerbation_4049 
probability that a person between 40 to 49 years will die of severe exacerbation 
Real 
0.02 
prob_will_die_sev_exacerbation_3039 
probability that a person between 30 to 39 years will die of severe exacerbation 
Real 
0.01 
prob_will_die_sev_exacerbation_lt30 
probability that a person less than 30 years will die of severe exacerbation 
Real 
0.0 
eff_oxygen 
the effect of oxygen on individuals with severe exacerbation 
Real 
0.6 
rel_risk_progress_per_higher_cat 
relative risk of progression to the next higher level of lung function for each higher level 
Real 
0.5 
rel_risk_tob 
relative effect of tobacco on the rate of lung function progression 
Real 
7.0 
rel_risk_wood_burn_stove 
relative risk of wood burn stove on the rate of lung function progression 
Real 
2.0 
prob_not_tob_lung_func_15_39 
probability of lung function categories in individuals aged 1539 and do not smoke tobacco 
List 
[0.496396, 0.337947, 0.114555, 0.040078, 0.010086, 0.000938, 0.0] 
prob_not_tob_lung_func_40_59 
probability of lung function categories in individuals aged 4059 and do not smoke tobacco 
List 
[0.114194, 0.306129, 0.292286, 0.212143, 0.067501, 0.007387, 0.00036] 
prob_not_tob_lung_func_gr59 
probability of lung function categories in individuals aged 60+ and do not smoke tobacco 
List 
[0.009201, 0.08707, 0.263341, 0.44523, 0.183632, 0.010073, 0.001453] 
prob_tob_lung_func_15_39 
probability of lung function categories in individuals aged 1539 who smoke tobacco 
List 
[0.06712, 0.199903, 0.259728, 0.241245, 0.148346, 0.071498, 0.01216] 
prob_tob_lung_func_40_59 
probability of lung function categories in individuals aged 4059 who smoke tobacco 
List 
[0.001499, 0.033733, 0.112819, 0.231259, 0.337331, 0.225637, 0.057722] 
prob_tob_lung_func_gr59 
probability of lung function categories in individuals aged 60+ who smoke tobacco 
List 
[0.0, 0.0, 0.035366, 0.20122, 0.453659, 0.246341, 0.063414] 
Demography
Name 
Description 
Type 
Value 

max_age_initial 
The oldest age (in whole years) in the initial population 
Integer 
120 
pop_2010 
Population in 2010 for initialising population 
Dataframe 

district_num_to_district_name 
Mapping from district_num to district name 
Dictionary 

district_num_to_region_name 
Mapping from district_num to region name 
Dictionary 

districts_in_region 
Set of districts (by name) that are within a region (by name) 
Dictionary 

all_cause_mortality_schedule 
Allcause agespecific mortality rates from WPP 
Dataframe 

fraction_of_births_male 
Birth Sex Ratio 
Series 
pop_2010
District 
District_Num 
Region 
Sex 
Age 
Count 

Chitipa 
0 
Northern 
M 
1 
3673.51 
Chitipa 
0 
Northern 
M 
2 
3538.09 
Chitipa 
0 
Northern 
M 
3 
3410.42 
Chitipa 
0 
Northern 
M 
4 
3289.97 
Chitipa 
0 
Northern 
M 
5 
3176.2 
Chitipa 
0 
Northern 
M 
6 
3068.58 
Chitipa 
0 
Northern 
M 
7 
2966.6 
Chitipa 
0 
Northern 
M 
8 
2869.74 
Chitipa 
0 
Northern 
M 
9 
2777.45 
Only first 10 rows of 6464 are shown.
district_num_to_district_name
0 
1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 
15 
16 
17 
18 
19 
20 
21 
22 
23 
24 
25 
26 
27 
28 
29 
30 
31 

Chitipa 
Karonga 
Nkhata Bay 
Rumphi 
Mzimba 
Likoma 
Mzuzu City 
Kasungu 
Nkhotakota 
Ntchisi 
Dowa 
Salima 
Lilongwe 
Mchinji 
Dedza 
Ntcheu 
Lilongwe City 
Mangochi 
Machinga 
Zomba 
Chiradzulu 
Blantyre 
Mwanza 
Thyolo 
Mulanje 
Phalombe 
Chikwawa 
Nsanje 
Balaka 
Neno 
Zomba City 
Blantyre City 
district_num_to_region_name
0 
1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 
15 
16 
17 
18 
19 
20 
21 
22 
23 
24 
25 
26 
27 
28 
29 
30 
31 

Northern 
Northern 
Northern 
Northern 
Northern 
Northern 
Northern 
Central 
Central 
Central 
Central 
Central 
Central 
Central 
Central 
Central 
Central 
Southern 
Southern 
Southern 
Southern 
Southern 
Southern 
Southern 
Southern 
Southern 
Southern 
Southern 
Southern 
Southern 
Southern 
Southern 
districts_in_region
Northern
0 
1 
2 
3 
4 
5 
6 

Rumphi 
Mzuzu City 
Nkhata Bay 
Chitipa 
Mzimba 
Likoma 
Karonga 
Central
0 
1 
2 
3 
4 
5 
6 
7 
8 
9 

Dowa 
Nkhotakota 
Salima 
Ntchisi 
Dedza 
Mchinji 
Kasungu 
Ntcheu 
Lilongwe 
Lilongwe City 
Southern
0 
1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 

Neno 
Chiradzulu 
Phalombe 
Blantyre 
Nsanje 
Balaka 
Mangochi 
Zomba City 
Chikwawa 
Blantyre City 
Mwanza 
Machinga 
Thyolo 
Mulanje 
Zomba 
all_cause_mortality_schedule
fallbackyear 
sex 
age_years 
death_rate 

1950 
M 
1 
0.0572109 
1950 
M 
2 
0.0572109 
1950 
M 
3 
0.0572109 
1950 
M 
4 
0.0572109 
1950 
M 
5 
0.0139565 
1950 
M 
6 
0.0139565 
1950 
M 
7 
0.0139565 
1950 
M 
8 
0.0139565 
1950 
M 
9 
0.0139565 
Only first 10 rows of 7200 are shown.
fraction_of_births_male
frac_births_male 

0.50495 
0.50495 
0.50495 
0.50495 
0.50495 
0.50495 
0.50495 
0.50495 
0.50495 
Only first 10 rows of 150 are shown.
Depression
Name 
Description 
Type 
Value 

init_pr_depr_m_age1519_no_cc_wealth123 
Initial probability of being depressed in male age1519 with no chronic condition with wealth level 1 or 2 or 3 
Real 
0.06 
init_rp_depr_f_not_rec_preg 
Initial relative prevalence of being depressed in females not recently pregnant 
Real 
1.5 
init_rp_depr_f_rec_preg 
Initial relative prevalence of being depressed in females recently pregnant 
Real 
3.0 
init_rp_depr_age2059 
Initial relative prevalence of being depressed in 2059 year olds vs 1519 
Real 
1.0 
init_rp_depr_agege60 
Initial relative prevalence of being depressed in 60+ year olds vs 1519 
Real 
3.0 
init_rp_depr_cc 
Initial relative prevalence of being depressed in people with chronic condition 
Real 
1.0 
init_rp_depr_wealth45 
Initial relative prevalence of being depressed in people with wealth level 4 or 5 vs 1 or 2 or 3 
Real 
1.0 
init_rp_ever_depr_per_year_older_m 
Initial relative prevalence ever depression per year older in men 
Real 
0.004 
init_rp_ever_depr_per_year_older_f 
Initial relative prevalence ever depression per year older in women 
Real 
0.006 
init_pr_ever_talking_therapy_if_diagnosed 
Initial probability of ever having had talking therapy if ever diagnosed with depression 
Real 
1.0 
init_pr_antidepr_curr_depr 
Initial probability of being on antidepressants if currently depressed 
Real 
0.11 
init_rp_antidepr_ever_depr_not_curr 
Initial relative prevalence of being on antidepressants if ever depressed but not currently 
Real 
0.5 
init_pr_ever_diagnosed_depression 
Initial probability of having ever been diagnosed with depression, amongst people with ever depression and not on antidepressants 
Real 
0.2 
init_pr_ever_self_harmed_if_ever_depr 
Initial probability of having ever self harmed if ever depressed 
Real 
0.004 
base_3m_prob_depr 
Probability of onset of depression in a 3 month period if male, wealth 1 2 or 3, no chronic condition and never previously depressed 
Real 
0.0021 
rr_depr_wealth45 
Relative rate of depression when in wealth level 4 or 5 vs 1 or 2 or 3 
Real 
3.0 
rr_depr_cc 
Relative rate of depression if has any chronic disease 
Real 
1.25 
rr_depr_pregnancy 
Relative rate of depression when pregnant or recently pregnant 
Real 
3.0 
rr_depr_female 
Relative rate of depression for females vs males 
Real 
1.5 
rr_depr_prev_epis 
Relative rate of depression associated with previous depression vs never previously depressed 
Real 
50.0 
rr_depr_on_antidepr 
Relative rate of depression episode if on antidepressants 
Real 
30.0 
rr_depr_age1519 
Relative rate of depression associated with 1520 year olds 
Real 
1.0 
rr_depr_agege60 
Relative rate of depression associated with age > 60 
Real 
3.0 
rr_depr_hiv 
Relative rate of depression associated with HIV infection 
Real 
1.99 
depr_resolution_rates 
Risk of depression resolving in 3 months if no chronic conditions and no treatments.Each individual is equally likely to be assigned each of these risks 
List 
[0.2, 0.3, 0.5, 0.7, 0.95] 
rr_resol_depr_cc 
Relative rate of resolving depression if has any chronic disease 
Real 
0.5 
rr_resol_depr_on_antidepr 
Relative rate of resolving depression if on antidepressants 
Real 
1.5 
rr_resol_depr_current_talk_ther 
Relative rate of resolving depression if has ever had talking therapy vs has never had talking therapy 
Real 
1.1 
prob_3m_stop_antidepr 
Probability per 3 months of stopping antidepressants when not currently depressed. 
Real 
0.7 
prob_3m_default_antidepr 
Probability per 3 months of stopping antidepressants when still depressed. 
Real 
0.2 
prob_3m_suicide_depr_m 
Probability per 3 months of suicide in currently depressed men 
Real 
0.0005 
rr_suicide_depr_f 
Relative risk of suicide in women compared with men 
Real 
0.333 
prob_3m_selfharm_depr 
Probability per 3 months of nonfatal self harm in those currently depressed 
Real 
0.0005 
sensitivity_of_assessment_of_depression 
The sensitivity of the clinical assessment in detecting the true current status of depression 
Real 
0.75 
pr_assessed_for_depression_in_generic_appt_level1 
Probability that a person is assessed for depression during a nonemergency generic appointmentlevel 1 
Real 
0.01 
anti_depressant_medication_item_code 
The item code used for one month of antidepressant treatment 
Integer 
267 
pr_assessed_for_depression_for_perinatal_female 
Probability that a perinatal female is assessed for depression during antenatal or postnatal services 
Real 
0.01 
Diarrhoea
Name 
Description 
Type 
Value 

base_inc_rate_diarrhoea_by_rotavirus 
incidence rate (per personyear) of diarrhoea caused by rotavirus in age groups 011, 1223, 2459 months 
List 
[0.175245863, 0.097007598, 0.009324] 
base_inc_rate_diarrhoea_by_shigella 
incidence rate (per personyear) of diarrhoea caused by shigella spp in age groups 011, 1223, 2459 months 
List 
[0.117936461999999, 0.078794104, 0.093018] 
base_inc_rate_diarrhoea_by_adenovirus 
incidence rate (per personyear) of diarrhoea caused by adenovirus 40/41 in age groups 011, 1223, 2459 months 
List 
[0.0586618, 0.058661803, 0.006438] 
base_inc_rate_diarrhoea_by_cryptosporidium 
incidence rate (per personyear) of diarrhoea caused by cryptosporidium in age groups 011, 1223, 2459 months 
List 
[0.030886699, 0.0117923629999999, 0.004662] 
base_inc_rate_diarrhoea_by_campylobacter 
incidence rate (per personyear) of diarrhoea caused by campylobacter spp in age groups 011, 1223, 2459 months 
List 
[0.098663257, 0.027915478, 0.004884] 
base_inc_rate_diarrhoea_by_ETEC 
incidence rate (per personyear) of diarrhoea caused by ETEC in age groups 011, 1223, 2459 months 
List 
[0.27925146, 0.170477152, 0.019758] 
base_inc_rate_diarrhoea_by_sapovirus 
incidence rate (per personyear) of diarrhoea caused by sapovirus in age groups 011, 1223, 2459 months 
List 
[0.100972179, 0.132603114, 0.00555] 
base_inc_rate_diarrhoea_by_norovirus 
incidence rate (per personyear) of diarrhoea caused by norovirus in age groups 011, 1223, 2459 months 
List 
[0.204864004, 0.066146727, 0.000888] 
base_inc_rate_diarrhoea_by_astrovirus 
incidence rate (per personyear) of diarrhoea caused by astrovirus in age groups 011, 1223, 2459 months 
List 
[0.054208352, 0.035974076, 0.001332] 
base_inc_rate_diarrhoea_by_tEPEC 
incidence rate (per personyear) of diarrhoea caused by tEPEC in age groups 011, 1223, 2459 months 
List 
[0.0608224569999999, 0.022716889, 0.001998] 
rr_diarrhoea_HHhandwashing 
relative rate of diarrhoea with household handwashing with soap 
Real 
0.7 
rr_diarrhoea_improved_sanitation 
relative rate of diarrhoea for improved sanitation 
Real 
0.75 
rr_diarrhoea_clean_water 
relative rate of diarrhoea for access to clean drinking water 
Real 
0.67 
rr_diarrhoea_exclusive_vs_partial_breastfeeding_<6mo 
relative rate of diarrhoea for partial breastfeeding in <6 months old, compared to exclusive breastfeeding 
Real 
1.68 
rr_diarrhoea_exclusive_vs_no_breastfeeding_<6mo 
relative rate of diarrhoea for no breastfeeding in <6 months old, compared to exclusive breastfeeding 
Real 
2.65 
rr_diarrhoea_any_vs_no_breastfeeding_6_11mo 
relative rate of diarrhoea for no breastfeeding in 6 months old to 1 years old, compared to any breastfeeding at this age group 
Real 
1.32 
rr_diarrhoea_untreated_HIV 
relative rate of diarrhoea for HIV positive status 
Real 
5.4 
rr_diarrhoea_SAM 
relative rate of diarrhoea for severe malnutrition 
Real 
1.2 
proportion_AWD_in_rotavirus 
acute diarrhoea type caused in rotavirusattributed diarrhoea 
Real 
0.97668 
proportion_AWD_in_shigella 
acute diarrhoea type caused in shigellaattributed diarrhoea 
Real 
0.861942 
proportion_AWD_in_adenovirus 
acute diarrhoea type caused in adenovirusattributed diarrhoea 
Real 
0.950061 
proportion_AWD_in_cryptosporidium 
acute diarrhoea type caused in cryptosporidiumattributed diarrhoea 
Real 
0.970984 
proportion_AWD_in_campylobacter 
acute diarrhoea type caused in campylobacterattributed diarrhoea 
Real 
0.896768 
proportion_AWD_in_ETEC 
acute diarrhoea type caused in ETECattributed diarrhoea 
Real 
0.950465 
proportion_AWD_in_sapovirus 
acute diarrhoea type caused in sapovirusattributed diarrhoea 
Real 
0.966385 
proportion_AWD_in_norovirus 
acute diarrhoea type caused in norovirusattributed diarrhoea 
Real 
0.961643 
proportion_AWD_in_astrovirus 
acute diarrhoea type caused in astrovirusattributed diarrhoea 
Real 
0.974147 
proportion_AWD_in_tEPEC 
acute diarrhoea type in tEPECattributed diarrhoea 
Real 
0.961485 
prob_dehydration_by_rotavirus 
probability of any dehydration caused by rotavirus 
Real 
0.153093 
prob_dehydration_by_shigella 
probability of any dehydration caused by shigella 
Real 
0.102962 
prob_dehydration_by_adenovirus 
probability of any dehydration caused by adenovirus 
Real 
0.079524 
prob_dehydration_by_cryptosporidium 
probability of any dehydration caused by cryptosporidium 
Real 
0.121458 
prob_dehydration_by_campylobacter 
probability of any dehydration caused by campylobacter 
Real 
0.072808 
prob_dehydration_by_ETEC 
probability of any dehydration caused by ETEC 
Real 
0.075925 
prob_dehydration_by_sapovirus 
probability of any dehydration caused by sapovirus 
Real 
0.10364 
prob_dehydration_by_norovirus 
probability of any dehydration caused by norovirus 
Real 
0.090728 
prob_dehydration_by_astrovirus 
probability of any dehydration caused by astrovirus 
Real 
0.122776 
prob_dehydration_by_tEPEC 
probability of any dehydration caused by tEPEC 
Real 
0.113362 
probability_of_severe_dehydration_if_some_dehydration 
probability that someone with diarrhoea and some dehydration develops severe dehydration 
Real 
0.167 
prob_prolonged_diarr_rotavirus 
probability of prolonged episode in rotavirusattributed diarrhoea 
Real 
0.117706 
prob_prolonged_diarr_shigella 
probability of prolonged episode by shigellaattributed diarrhoea 
Real 
0.165342 
prob_prolonged_diarr_adenovirus 
probability of prolonged episode by adenovirusattributed diarrhoea 
Real 
0.116406 
prob_prolonged_diarr_cryptosporidium 
probability of prolonged episode by cryptosporidiumattributed diarrhoea 
Real 
0.169134 
prob_prolonged_diarr_campylobacter 
probability of prolonged episode by campylobacterattributed diarrhoea 
Real 
0.152206 
prob_prolonged_diarr_ETEC 
probability of prolonged episode by ETECattributed diarrhoea 
Real 
0.114177 
prob_prolonged_diarr_sapovirus 
probability of prolonged episode by sapovirusattributed diarrhoea 
Real 
0.133209 
prob_prolonged_diarr_norovirus 
probability of prolonged episode by norovirusattributed diarrhoea 
Real 
0.118223 
prob_prolonged_diarr_astrovirus 
probability of prolonged episode by norovirusattributed diarrhoea 
Real 
0.13511 
prob_prolonged_diarr_tEPEC 
probability of prolonged episode by tEPECattributed diarrhoea 
Real 
0.190845 
prob_prolonged_to_persistent_diarr 
probability of prolonged diarrhoea becoming persistent diarrhoea 
Real 
0.2866 
rr_bec_persistent_age>6mo 
relative rate of acute diarrhoea becoming persistent diarrhoea for children over 6 months 
Real 
0.26 
rr_bec_persistent_HIV 
relative rate of acute diarrhoea becoming persistent diarrhoea for HIV positive 
Real 
1.7 
rr_bec_persistent_SAM 
relative rate of acute diarrhoea becoming persistent diarrhoea for severely acute malnutrition 
Real 
1.7 
rr_bec_persistent_stunted 
relative rate of acute diarrhoea becoming persistent diarrhoea for stunted children 
Real 
33.3 
min_dur_acute 
The minimum duration (in days) for an episode that is classified as an acute episode 
Integer 
1 
min_dur_prolonged 
The minimum duration (in days) for an episode that is classified as a prolonged episode 
Integer 
5 
min_dur_persistent 
The minimum duration (in days) for an episode that is classified as a persistent episode 
Integer 
13 
max_dur_persistent 
The maximum duration (in days) for an episode that is classified as a persistent episode 
Integer 
30 
prob_fever_by_rotavirus 
probability of fever caused by rotavirus 
Real 
0.384925 
prob_fever_by_shigella 
probability of fever caused by shigella 
Real 
0.319876 
prob_fever_by_adenovirus 
probability of fever caused by adenovirus 
Real 
0.271513 
prob_fever_by_cryptosporidium 
probability of fever caused by cryptosporidium 
Real 
0.322385 
prob_fever_by_campylobacter 
probability of fever caused by campylobacter 
Real 
0.312807 
prob_fever_by_ETEC 
probability of fever caused by ETEC 
Real 
0.258931 
prob_fever_by_sapovirus 
probability of fever caused by sapovirus 
Real 
0.292276 
prob_fever_by_norovirus 
probability of fever caused by norovirus 
Real 
0.251071 
prob_fever_by_astrovirus 
probability of fever caused by astrovirus 
Real 
0.195905 
prob_fever_by_tEPEC 
probability of fever caused by tEPEC 
Real 
0.384547 
prob_vomiting_by_rotavirus 
probability of vomiting caused by rotavirus 
Real 
0.471793 
prob_vomiting_by_shigella 
probability of vomiting caused by shigella 
Real 
0.209852 
prob_vomiting_by_adenovirus 
probability of vomiting caused by adenovirus 
Real 
0.308677 
prob_vomiting_by_cryptosporidium 
probability of vomiting caused by cryptosporidium 
Real 
0.243581 
prob_vomiting_by_campylobacter 
probability of vomiting caused by campylobacter 
Real 
0.218669 
prob_vomiting_by_ETEC 
probability of vomiting caused by ETEC 
Real 
0.283139 
prob_vomiting_by_sapovirus 
probability of vomiting caused by sapovirus 
Real 
0.303154 
prob_vomiting_by_norovirus 
probability of vomiting caused by norovirus 
Real 
0.299343 
prob_vomiting_by_astrovirus 
probability of vomiting caused by astrovirus 
Real 
0.276018 
prob_vomiting_by_tEPEC 
probability of vomiting caused by tEPEC 
Real 
0.285661 
adjustment_factor_on_cfr 
Factor by which fatality probabilities are multiplied (to be used in calibration) 
Real 
3.75 
case_fatality_rate_AWD 
case fatality rate for acute watery diarrhoea cases 
Real 
0.0015 
rr_diarr_death_bloody 
relative risk of diarrhoea death (compared to case_fatality_rate_AWD if the diarrhoea is of type “bloody” (i.e. dyssentry). 
Real 
7.6 
rr_diarr_death_age24to59mo 
relative risk of diarrhoea death for ages 24 to 59 months 
Real 
0.38 
rr_diarr_death_if_duration_longer_than_13_days 
relative risk of diarrhoea death if the duration episode is 13 days or longer 
Real 
0.0035 
rr_diarr_death_severe_dehydration 
relative risk of diarrhoea death for cases with severe dehyadration 
Real 
3.45 
rr_diarr_death_untreated_HIV 
relative risk of diarrhoea death for untreated HIV 
Real 
5.05 
rr_diarr_death_SAM 
relative risk of diarrhoea death for severe acute malnutrition 
Real 
4.13 
rr_diarr_death_alri 
relative risk of diarrhoea death if concurrent lower respiratory infection 
Real 
3.51 
rr_diarr_death_cryptosporidium 
relative risk of diarrhoea death if caused by cryptosporidium 
Real 
2.14 
rr_diarr_death_shigella 
relative risk of diarrhoea death if caused by shigella 
Real 
2.8 
sensitivity_severe_dehydration_visual_inspection 
sensitivity of IMCI severe dehydration algorithm for dehydration >9% loss of body weight 
Real 
0.77 
specificity_severe_dehydration_visual_inspection 
specificity of IMCI severe dehydration algorithm for dehydration >9% loss of body weight 
Real 
0.67 
prob_hospitalization_on_danger_signs 
probability of hospitalisation when danger signs are detected in an initial consultation 
Real 
0.7 
prob_WHOPlanC_cures_dehydration_if_severe_dehydration 
probability that severe dehydration is cured by Treatment Plan C 
Real 
0.9 
prob_ORS_cures_dehydration_if_severe_dehydration 
probability that severe dehydration is cured by ORS 
Real 
0.721 
prob_ORS_cures_dehydration_if_non_severe_dehydration 
probability that nonsevere dehydration is cured by ORS 
Real 
0.93 
prob_antibiotic_cures_dysentery 
probability that bloodinstool is removed by the use of antibiotics 
Real 
0.99 
number_of_days_reduced_duration_with_zinc 
number of days reduced duration with zinc 
Integer 
1 
days_between_treatment_and_cure 
number of days between any treatment being given in an HSI and the cure occurring. 
Integer 
5 
rr_severe_dehydration_due_to_rotavirus_with_R1_under1yo 
relative risk of severe dehydration with rotavirus vaccine, for under 1 years old. 
Real 
0.63 
rr_severe_dehydration_due_to_rotavirus_with_R1_over1yo 
relative risk of severe dehydration with rotavirus vaccine, for those aged 1 year and older. 
Real 
0.35 
Epi
Name 
Description 
Type 
Value 

baseline_coverage 
baseline vaccination coverage (all vaccines) 
Dataframe 

vaccine_schedule 
vaccination schedule applicable from 2018 onwards 
Series 

prob_facility_level_for_vaccine 
The probability of going to each facilitylevel (0 / 1a / 1b / 2) for child having vaccines given through childhood immunisation schedule. The probabilities must sum to 1.0 
List 
[0, 0.8, 0.1, 0.1] 
baseline_coverage
Year 
BCG 
DTP1 
DTP3 
HepB3 
Hib3 
MCV1 
MCV2 
PCV3 
Pol3 
RCV1 
Rota 
IPV1 
AgeOn01Jan2010 

1981 
0.86 
0.86 
0.66 
0 
0 
0.64 
0 
0 
0.57 
0 
0 
0 
28 
1982 
0.87 
0.84 
0.64 
0 
0 
0.64 
0 
0 
0.58 
0 
0 
0 
27 
1983 
0.81 
0.84 
0.63 
0 
0 
0.58 
0 
0 
0.58 
0 
0 
0 
26 
1984 
0.74 
0.8 
0.58 
0 
0 
0.5 
0 
0 
0.56 
0 
0 
0 
25 
1985 
0.87 
0.78 
0.55 
0 
0 
0.49 
0 
0 
0.55 
0 
0 
0 
24 
1986 
0.87 
0.8 
0.57 
0 
0 
0.6 
0 
0 
0.53 
0 
0 
0 
23 
1987 
0.92 
0.92 
0.78 
0 
0 
0.79 
0 
0 
0.78 
0 
0 
0 
22 
1988 
0.9 
0.94 
0.82 
0 
0 
0.82 
0 
0 
0.72 
0 
0 
0 
21 
1989 
0.96 
0.95 
0.87 
0 
0 
0.84 
0 
0 
0.9 
0 
0 
0 
20 
Only first 10 rows of 42 are shown.
vaccine_schedule
date_administration_days 

1 
42 
70 
98 
42 
70 
98 
42 
70 
Only first 10 rows of 21 are shown.
Epilepsy
Name 
Description 
Type 
Value 

init_epil_seiz_status 
Proportions in each seizure status category at baseline 
List 
[0.974, 0.0175, 0.007, 0.0015] 
init_prop_antiepileptic_seiz_stat_1 
initial proportions on antiepileptic by if seizure status = 1 
Real 
0.15 
init_prop_antiepileptic_seiz_stat_2 
initial proportions on antiepileptic by if seizure status = 2 
Real 
0.15 
init_prop_antiepileptic_seiz_stat_3 
initial proportions on antiepileptic by if seizure status = 3 
Real 
0.2 
base_3m_prob_epilepsy 
base probability of epilepsy per 3 month period if age < 20 
Real 
0.000178 
rr_epilepsy_age_ge20 
relative rate of epilepsy if age over 20 
Real 
0.3 
prop_inc_epilepsy_seiz_freq 
proportion of incident epilepsy cases with frequent seizures 
Real 
0.1 
base_prob_3m_seiz_stat_freq_infreq 
base probability per 3 months of seizure status frequent if current infrequent 
Real 
0.05 
rr_effectiveness_antiepileptics 
relative rate of seizure status frequent if current infrequent if on antiepileptic 
Real 
3.0 
base_prob_3m_seiz_stat_infreq_freq 
base probability per 3 months of seizure status infrequent if current frequent 
Real 
0.05 
base_prob_3m_seiz_stat_infreq_none 
base probability per 3 months of seizure status infrequent if current nonenow 
Real 
0.05 
base_prob_3m_seiz_stat_none_freq 
base probability per 3 months of seizure status nonenow if current frequent 
Real 
0.05 
base_prob_3m_seiz_stat_none_infreq 
base probability per 3 months of seizure status nonenow if current infrequent 
Real 
0.05 
base_prob_3m_stop_antiepileptic 
base probability per 3 months of stopping antiepileptic, if nonenow seizures 
Real 
0.05 
rr_stop_antiepileptic_seiz_infreq_or_freq 
relative rate of stopping antiepileptic if infrequent or frequent seizures 
Real 
1.0 
base_prob_3m_epi_death 
base probability per 3 months of epilepsy death 
Real 
0.000568 
daly_wt_epilepsy_severe 
disability weight for severe epilepsycontrolled phase  code 860 
Real 
0.552 
daly_wt_epilepsy_less_severe 
disability weight for less severe epilepsycontrolled phase  code 861 
Real 
0.263 
daly_wt_epilepsy_seizure_free 
disability weight for less severe epilepsycontrolled phase  code 862 
Real 
0.049 
HealthSeekingBehaviour
Name 
Description 
Type 
Value 

force_any_symptom_to_lead_to_healthcareseeking 
Whether every symptom [except those that declare they should not lead to any healthcare seeking] should always lead to healthcare seeking immediately. 
Boolean 
False 
prob_non_emergency_care_seeking_by_level 
The probability of going to each facilitylevel when nonemergency care is sought. The values in the list are the probabilities of going to facility level 0 / 1a / 1b / 2, respectively, and these values must sum to 1.0. 
List 
[0.14, 0.66, 0.08, 0.12] 
baseline_odds_of_healthcareseeking_children 
odds of healthcare seeking (children: 014) if male, 05 yearsold, living in a rural setting in the Northern region, and not in the wealth categories 4 or 5 
Real 
2.17 
odds_ratio_children_sex_Female 
odds ratio for healthcare seeking (children) if sex is Female 
Real 
1.12 
odds_ratio_children_age_5to14 
odds ratio for healthcare seeking (children) if aged 514 
Real 
0.5 
odds_ratio_children_setting_urban 
odds ratio for healthcare seeking (children) if setting is Urban 
Real 
1.75 
odds_ratio_children_region_Central 
odds ratio for healthcare seeking (children) if region is Central 
Real 
0.43 
odds_ratio_children_region_Southern 
odds ratio for healthcare seeking (children) if region is Southern 
Real 
0.56 
odds_ratio_children_wealth_higher 
odds ratio for healthcare seeking (children) if wealth is in categories 4 or 5 
Real 
1.9 
baseline_odds_of_healthcareseeking_adults 
odds of healthcare seeking (adults: 15+) if male, 1534 yearolds, living in a rural setting in the Northern region, and not in the wealth categories 4 or 5. 
Real 
1.27 
odds_ratio_adults_sex_Female 
odds ratio for healthcare seeking (adults) if sex is Female 
Real 
1.28 
odds_ratio_adults_age_35to59 
odds ratio for healthcare seeking (adults) if aged 3559 
Real 
0.93 
odds_ratio_adults_age_60plus 
odds ratio for healthcare seeking (adults) if aged 60+ 
Real 
0.94 
odds_ratio_adults_setting_urban 
odds ratio for healthcare seeking (adults) if setting is Urban 
Real 
1.67 
odds_ratio_adults_region_Central 
odds ratio for healthcare seeking (adults) if region is Central 
Real 
0.6 
odds_ratio_adults_region_Southern 
odds ratio for healthcare seeking (adults) if region is Southern 
Real 
0.68 
odds_ratio_adults_wealth_higher 
odds ratio for healthcare seeking (adults) if wealth is in categories 4 or 5 
Real 
1.56 
max_days_delay_to_generic_HSI_after_symptoms 
Maximum days delay between symptom onset and firstgeneric HSI. Actual delay is sample between 0 and this value. 
Integer 
4 
HealthSystem
Name 
Description 
Type 
Value 

Master_Facilities_List 
Listing of all health facilities. 
Dataframe 

Officer_Types_Table 
The names of the types of health workers (“officers”) 
Dataframe 

Appt_Types_Table 
The names of the type of appointments with the health system 
Dataframe 

Appt_Offered_By_Facility_Level 
Table indicating whether or not each appointment is offered at each facility level. 
Dataframe 

Appt_Time_Table 
The time taken for each appointment, according to officer and facility type. 
Dataframe 

Daily_Capabilities_actual 
The capabilities (minutes of time available of each type of officer in each facility) based on the _estimated current_ number and distribution of staff estimated. 
Dataframe 

Daily_Capabilities_funded 
The capabilities (minutes of time available of each type of officer in each facility) based on the _potential_ number and distribution of staff estimated (i.e. those positions that can be funded). 
Dataframe 

Daily_Capabilities_funded_plus 
The capabilities (minutes of time available of each type of officer in each facility) based on the _potential_ number and distribution of staff estimated, with adjustments to permit each appointment type that should be run at facility level to do so in every district. 
Dataframe 

use_funded_or_actual_staffing 
If actual, then use the numbers and distribution of staff estimated to be available currently; If funded, then use the numbers and distribution of staff that are potentially available. If funded_plus, then use a dataset in which the allocation of staff to facilities is tweaked so as to allow each appointment type to run at each facility_level in each district for which it is defined. N.B. This parameter is overridden if an argument is provided to the module initialiser. 
String 
actual 
item_and_package_code_lookups 
Data imported from the OneHealth Tool on consumable items, packages and costs. 
Dataframe 

consumables_item_designations 
Lookup table for the designations of consumables (whether diagnostic, medicine, or other 
Dataframe 

availability_estimates 
Estimated availability of consumables in the LMIS dataset. 
Dataframe 

cons_availability 
Availability of consumables. If ‘default’ then use the availability specified in the ResourceFile; if ‘none’, then let no consumable be ever be available; if ‘all’, then all consumables are always available. When using ‘all’ or ‘none’, requests for consumables are not logged. NB. This parameter is overriddenif an argument is provided to the module initialiser.Note that other options are also available: see the Consumables class. 
String 
default 
BedCapacity 
Data on the number of beds available of each type by facility_id 
Dataframe 

beds_availability 
Availability of beds. If ‘default’ then use the availability specified in the ResourceFile; if ‘none’, then let no beds be ever be available; if ‘all’, then all beds are always available. NB. This parameter is overridden if an argument is provided to the module initialiser. 
String 
default 
EquipmentCatalogue 
Data on equipment items and packages. 
Dataframe 

equipment_availability_estimates 
Data on the availability of equipment items and packages. 
Dataframe 

equip_availability 
What to assume about the availability of equipment. If ‘default’ then use the availability specified in the ResourceFile; if ‘none’, then let no equipment ever be available; if ‘all’, then all equipment is always available. NB. This parameter is overridden if an argument is provided to the module initialiser. 
String 
all 
equip_availability_postSwitch 
What to assume about the availability of equipment after the switch (see year_equip_availability_switch). The options for this are the same as equip_availability. 
String 
default 
year_equip_availability_switch 
Year in which the assumption for equip_availability changes (The change happens on 1st January of that year.) 
Integer 
2100 
Service_Availability 
List of services to be available. NB. This parameter is overridden if an argument is provided to the module initialiser. 
List 
[‘*’] 
policy_name 
Name of priority policy adopted 
String 
Naive 
year_mode_switch 
Year in which mode switch is enforced 
Integer 
2100 
scale_to_effective_capabilities 
In year in which mode switch takes place, will rescale available capabilities to match thosethat were effectively used (on average) in the past year if this is set to True. This way,we can approximate overtime and rushing of appts even in mode 2. 
Boolean 
False 
year_cons_availability_switch 
Year in which consumable availability switch is enforced. The change happenson 1st January of that year.) 
Integer 
2100 
year_use_funded_or_actual_staffing_switch 
Year in which switch for use_funded_or_actual_staffing is enforced. (The change happenson 1st January of that year.) 
Integer 
2100 
priority_rank 
Data on the priority ranking of each of the Treatment_IDs to be adopted by the queueing system under different policies, where the lower the number the higher the priority, and on which categories of individuals classify for fasttracking for specific treatments 
Dictionary 

HR_scaling_by_level_and_officer_type_table 
Factors by which capabilities of medical officer types at different levels will bescaled at the start of the year specified by year_HR_scaling_by_level_and_officer_type. Thisserves to simulate a number of effects (e.g. absenteeism, boosting capabilities of specific medical cadres, etc). This is the imported from an Excel workbook: keys are the worksheet names and values are the worksheets in the format of pd.DataFrames. Additional scenarios can be added by adding worksheets to this workbook: the value of HR_scaling_by_level_and_officer_type_mode indicates which sheet is used. 
Dictionary 

year_HR_scaling_by_level_and_officer_type 
Year in which oneoff constant HR scaling will take place. (The change happenson 1st January of that year.) 
Integer 
2100 
HR_scaling_by_level_and_officer_type_mode 
Mode of HR scaling considered at the start of the simulation. This corresponds to the nameof the worksheet in ResourceFile_HR_scaling_by_level_and_officer_type.xlsx that should be used. Options are: default (capabilities are scaled by a constaint factor of 1); data (factors informed by survey data); and, custom (user can freely set these factors as parameters in the analysis). 
String 
default 
HR_scaling_by_district_table 
Factors by which daily capabilities in different districts will bescaled at the start of the year specified by year_HR_scaling_by_district to simulate(e.g., through catastrophic event disrupting delivery of services in particular district(s)).This is the import of an Excel workbook: keys are the worksheet names and values are the worksheets in the format of pd.DataFrames. Additional scenarios can be added by adding worksheets to this workbook: the value of HR_scaling_by_district_mode indicates whichsheet is used. 
Dictionary 

year_HR_scaling_by_district 
Year in which scaling of daily capabilities by district will take place. (The change happenson 1st January of that year.) 
Integer 
2100 
HR_scaling_by_district_mode 
Mode of scaling of daily capabilities by district. This corresponds to the name of the worksheet in the file ResourceFile_HR_scaling_by_district.xlsx. 
String 
default 
yearly_HR_scaling 
Factors by which HR capabilities are scaled. Each sheet specifies a ‘mode’ for dynamic HR scaling. The mode to use is determined by the parameter yearly_HR_scaling_mode. Each sheet must have the same format, including the same column headers. On each sheet, the first row (for 2010, when the simulation starts) specifies the initial configuration: dynamic_HR_scaling_factor (float) is the factor by which all human resoucres capabilities and multiplied; scale_HR_by_popsize (bool) specifies whether the capabilities should (also) grow by the factor by which the population has grown in the last year. Each subsequent row specifies a year where there should be a CHANGE in the configuration. If there are no further rows, then there is no change. But, for example, an additional row of the form 
Dictionary 

yearly_HR_scaling_mode 
Specifies which of the policies in yearly_HR_scaling should be adopted. This corresponds toa worksheet of the file ResourceFile_dynamic_HR_scaling.xlsx. 
String 
no_scaling 
tclose_overwrite 
Decide whether to overwrite tclose variables assigned by disease modules 
Integer 
0 
tclose_days_offset_overwrite 
Offset in days from topen at which tclose will be set by the healthsystem for all HSIsif tclose_overwrite is set to True. 
Integer 
7 
mode_appt_constraints 
Integer code in {0, 1, 2} determining mode of constraints with regards to officer numbers and time  0: no constraints, all HSI events run with no squeeze factor, 1: elastic constraints, all HSI events run with squeeze factor, 2: hard constraints, only HSI events with no squeeze factor run. N.B. This parameter is overridden if an argument is provided to the module initialiser. 
Integer 
1 
mode_appt_constraints_postSwitch 
Mode considered after a mode switch in year_mode_switch. 
Integer 
1 
cons_availability_postSwitch 
Consumables availability after switch in year_cons_availability_switch. Acceptable valuesare the same as those for Parameter cons_availability. 
String 
default 
use_funded_or_actual_staffing_postSwitch 
Staffing availability after switch in year_use_funded_or_actual_staffing_switch. Acceptable values are the same as those for Parameter use_funded_or_actual_staffing. 
String 
funded_plus 
Master_Facilities_List
District 
Facility_Level 
Region 
Facility_ID 
Facility_Name 

Balaka 
1a 
Southern 
1 
Facility_Level_1a_Balaka 
Balaka 
1b 
Southern 
2 
Facility_Level_1b_Balaka 
Balaka 
2 
Southern 
3 
Facility_Level_2_Balaka 
Blantyre 
0 
Southern 
4 
Facility_Level_0_Blantyre 
Blantyre 
1a 
Southern 
5 
Facility_Level_1a_Blantyre 
Blantyre 
1b 
Southern 
6 
Facility_Level_1b_Blantyre 
Blantyre 
2 
Southern 
7 
Facility_Level_2_Blantyre 
Blantyre City 
0 
Southern 
8 
Facility_Level_0_Blantyre City 
Blantyre City 
1a 
Southern 
9 
Facility_Level_1a_Blantyre City 
Only first 10 rows of 133 are shown.
Officer_Types_Table
Officer_Type 
Officer_Type_Code 
Officer_Category 

Clinical Officer / Technician 
M02 
Clinical 
Med. Assistant 
M03 
Clinical 
Nurse Officer 
N01 
Nursing_and_Midwifery 
Nurse Midwife Technician 
N02 
Nursing_and_Midwifery 
Pharmacist 
P01 
Pharmacy 
Pharm Technician 
P02 
Pharmacy 
Pharm Assistant 
P03 
Pharmacy 
Lab Officer 
L01 
Laboratory 
Lab Technician 
L02 
Laboratory 
Only first 10 rows of 21 are shown.
Appt_Types_Table
Appt_Type_Code 
Appt_Cat 
Appt_Type 

IPAdmission 
GENERAL_INPATIENT_AND_OUTPATIENT_CARE 
Inpatient Admissions and Discharge Process 
Under5OPD 
GENERAL_INPATIENT_AND_OUTPATIENT_CARE 
Under 5 Outpatient Visit 
Over5OPD 
GENERAL_INPATIENT_AND_OUTPATIENT_CARE 
Over 5 Outpatient visit 
NormalDelivery 
RMNCH 
Normal Deliveries 
CompDelivery 
RMNCH 
Complicated Deliveries 
Csection 
RMNCH 
Caesarean Sections 
FamPlan 
RMNCH 
Family Planning 
AntenatalFirst 
RMNCH 
Antenatal Care  First Visit 
ANCSubsequent 
RMNCH 
Antenatal Care  Followup Visit 
Only first 10 rows of 50 are shown.
Appt_Offered_By_Facility_Level
Appt_Type_Code 
Facility_Level_0 
Facility_Level_1a 
Facility_Level_1b 
Facility_Level_2 
Facility_Level_3 
Facility_Level_4 
Facility_Level_5 

IPAdmission 
False 
True 
True 
True 
True 
False 
False 
Under5OPD 
False 
True 
True 
True 
True 
False 
False 
Over5OPD 
False 
True 
True 
True 
True 
False 
False 
NormalDelivery 
False 
True 
True 
True 
True 
False 
False 
CompDelivery 
False 
True 
True 
True 
True 
False 
False 
Csection 
False 
True 
True 
True 
True 
False 
False 
FamPlan 
False 
True 
True 
True 
False 
False 
False 
AntenatalFirst 
False 
True 
True 
True 
True 
False 
False 
ANCSubsequent 
False 
True 
True 
True 
True 
False 
False 
Only first 10 rows of 50 are shown.
Appt_Time_Table
Appt_Type_Code 
Facility_Level 
Officer_Category 
Time_Taken_Mins 

ANCSubsequent 
2 
Nursing_and_Midwifery 
18 
ANCSubsequent 
2 
Pharmacy 
1 
ANCSubsequent 
3 
Clinical 
3 
ANCSubsequent 
3 
Nursing_and_Midwifery 
15 
ANCSubsequent 
3 
Pharmacy 
5 
ANCSubsequent 
1a 
Clinical 
1 
ANCSubsequent 
1a 
Nursing_and_Midwifery 
11 
ANCSubsequent 
1a 
Pharmacy 
0.4 
ANCSubsequent 
1b 
Clinical 
2 
Only first 10 rows of 345 are shown.
Daily_Capabilities_actual
Facility_ID 
Facility_Name 
Facility_Level 
District 
Region 
Officer_Category 
Total_Mins_Per_Day 
Staff_Count 

0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
DCSA 
17362.5 
311 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Dental 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Laboratory 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Mental 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Nursing_and_Midwifery 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Nutrition 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Pharmacy 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Radiography 
0 
0 
1 
Facility_Level_1a_Balaka 
1a 
Balaka 
Southern 
Clinical 
7764.57 
35.9682 
Only first 10 rows of 1197 are shown.
Daily_Capabilities_funded
Facility_ID 
Facility_Name 
Facility_Level 
District 
Region 
Officer_Category 
Total_Mins_Per_Day 
Staff_Count 

0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
DCSA 
13957 
250 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Dental 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Laboratory 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Mental 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Nursing_and_Midwifery 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Nutrition 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Pharmacy 
0 
0 
0 
Facility_Level_0_Balaka 
0 
Balaka 
Southern 
Radiography 
0 
0 
1 
Facility_Level_1a_Balaka 
1a 
Balaka 
Southern 
Clinical 
9786.98 
47.0287 
Only first 10 rows of 1197 are shown.
Daily_Capabilities_funded_plus
Facility_ID 
Facility_Name 
Facility_Level 
District 
Region 
Officer_Category 
Total_Mins_Per_Day 
Staff_Count 

1 
Facility_Level_1a_Balaka 
1a 
Balaka 
Southern 
Clinical 
9786.98 
47.0287 
1 
Facility_Level_1a_Balaka 
1a 
Balaka 
Southern 
Dental 
2327.32 
11.3933 
1 
Facility_Level_1a_Balaka 
1a 
Balaka 
Southern 
Laboratory 
5012.02 
24.9123 
1 
Facility_Level_1a_Balaka 
1a 
Balaka 
Southern 
Nursing_and_Midwifery 
31874.9 
150.48 
1 
Facility_Level_1a_Balaka 
1a 
Balaka 
Southern 
Nutrition 
110.791 
0.542373 
1 
Facility_Level_1a_Balaka 
1a 
Balaka 
Southern 
Pharmacy 
4132.1 
20.6361 
2 
Facility_Level_1b_Balaka 
1b 
Balaka 
Southern 
Clinical 
6470 
31.8781 
2 
Facility_Level_1b_Balaka 
1b 
Balaka 
Southern 
Dental 
719.736 
3.52345 
2 
Facility_Level_1b_Balaka 
1b 
Balaka 
Southern 
Laboratory 
1340.35 
5.95697 
Only first 10 rows of 733 are shown.
item_and_package_code_lookups
Intervention_Cat 
Intervention_Pkg 
Intervention_Pkg_Code 
Items 
Item_Code 
Expected_Units_Per_Case 
Unit_Cost 

Maternal/Newborn and Reproductive Health 
Pill 
0 
Levonorgestrel 0.15 mg + Ethinyl estradiol 30 mcg (Microgynon), cycle 
1 
7.5 
53.3501 
Maternal/Newborn and Reproductive Health 
Male condom 
1 
Condom, male 
2 
120 
20.9702 
Maternal/Newborn and Reproductive Health 
Injectable 
2 
DepotMedroxyprogesterone Acetate 150 mg  3 monthly 
3 
4 
50.9439 
Maternal/Newborn and Reproductive Health 
Injectable 
2 
Gloves, exam, latex, disposable, pair 
4 
4 
31.9087 
Maternal/Newborn and Reproductive Health 
Injectable 
2 
Povidone iodine, solution, 10 %, 5 ml per injection 
5 
4 
2.00634 
Maternal/Newborn and Reproductive Health 
Injectable 
2 
Syringe, Autodisable SoloShot IX 
6 
4 
5.4264 
Maternal/Newborn and Reproductive Health 
IUD 
3 
Gloves, exam, latex, disposable, pair 
4 
3 
31.9087 
Maternal/Newborn and Reproductive Health 
IUD 
3 
IUD, Copper T380A 
7 
1 
19.3922 
Maternal/Newborn and Reproductive Health 
Implant 
4 
Gloves, exam, latex, disposable, pair 
4 
2 
31.9087 
Only first 10 rows of 2444 are shown.
consumables_item_designations
is_diagnostic 
is_medicine 
is_other 
is_vital 
is_drug_or_vaccine 

0 
0 
1 
1 
0 
0 
1 
0 
1 
1 
0 
0 
1 
1 
0 
0 
1 
0 
1 
0 
0 
0 
1 
1 
0 
0 
1 
0 
1 
0 
0 
1 
0 
0 
1 
0 
0 
1 
1 
0 
0 
0 
1 
1 
0 
Only first 10 rows of 2016 are shown.
availability_estimates
Facility_ID 
month 
item_code 
available_prop 

0 
1 
1 
0.3825 
0 
1 
2 
0.555 
0 
1 
3 
0.33875 
0 
1 
5 
0.145161 
0 
1 
6 
0.609167 
0 
1 
7 
0.4 
0 
1 
8 
0 
0 
1 
11 
0.25 
0 
1 
12 
0.357143 
Only first 10 rows of 307296 are shown.
BedCapacity
Facility_ID 
maternity_bed 
delivery_bed 
general_bed 
non_bed_space 

1 
134 
29 
14 
1000 
2 
49 
6 
57 
1000 
3 
35 
4 
54 
1000 
4 
0 
0 
0 
0 
5 
168 
32 
50 
1000 
6 
61 
7 
195 
1000 
7 
44 
4 
184 
1000 
8 
0 
0 
0 
0 
9 
168 
32 
50 
1000 
Only first 10 rows of 133 are shown.
EquipmentCatalogue
Item_Description 
Item_Code 
Pkg_Name 
Source_Equip_Item 
Alternative item names 

Weighing scale 
1 
ANC 
Malawi HSSPIII Equipment Costing 2023 
‘Salter weighing scale’, ‘Waeighing Scale’ 
Autoclave 
2 
nan 
Malawi HSSPIII Equipment Costing 2023 
‘High pressure cooker sterilizer, complete with stove’, ‘Sterilization drums, medium’, ‘Sterilization drum’, ‘Sterilization buckets’, ‘Sterilization buckets (decontamination buckets)’, ‘Sterilization Buckets’, ‘Decontamination drums’, ‘Dressing drum medium’, ‘Dressing drum large’, ‘Dressing drum small’ 
Refrigerator 
3 
nan 
Malawi HSSPIII Equipment Costing 2023 
‘Vaccine refrigerator (solar)’, ‘Vaccine Refrigerator’ 
Cold box 
4 
nan 
Malawi HSSPIII Equipment Costing 2023 
‘Cold Chain Boxlarge’, ‘Cold Chain Boxmedium’ 
Vaccine Carriers 
5 
nan 
Malawi HSSPIII Equipment Costing 2023 
nan 
Blood pressure machine 
6 
Minor Surgery, Major Surgery, ICU 
Malawi HSSPIII Equipment Costing 2023 
nan 
Thermometer 
7 
nan 
Malawi HSSPIII Equipment Costing 2023 
‘Thermometers, digital’ 
Push bike for mobility 
8 
nan 
Malawi HSSPIII Equipment Costing 2023 
nan 
Desk 
9 
nan 
Malawi HSSPIII Equipment Costing 2023 
‘Office desk’ 
Only first 10 rows of 404 are shown.
equipment_availability_estimates
Facility_ID 
Item_Code 
Pr_Available 

0 
1 
0.75 
0 
2 
1 
0 
3 
1 
0 
4 
0.226281 
0 
5 
0.226281 
0 
6 
0.25 
0 
7 
0.75 
0 
8 
0.226281 
0 
9 
0.226281 
Only first 10 rows of 53732 are shown.
priority_rank
Default
Treatment 
Priority 
FT_if_5orUnder 
FT_if_pregnant 
FT_if_tbdiagnosed 
FT_if_Hivdiagnosed 

FirstAttendance_SpuriousEmergencyCare 
0 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Outpatient 
0 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient 
0 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient_Followup 
0 
1 
1 
1 
1 
BladderCancer_Investigation 
0 
1 
1 
1 
1 
BladderCancer_PalliativeCare 
0 
1 
1 
1 
1 
BladderCancer_Treatment 
0 
1 
1 
1 
1 
BreastCancer_Investigation 
0 
1 
1 
1 
1 
BreastCancer_PalliativeCare 
0 
1 
1 
1 
1 
Only first 10 rows of 87 are shown.
Test
Treatment 
Priority 
FT_if_5orUnder 
FT_if_pregnant 
FT_if_tbdiagnosed 
FT_if_Hivdiagnosed 

FirstAttendance_SpuriousEmergencyCare 
0 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Outpatient 
0 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient 
0 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient_Followup 
0 
1 
1 
1 
1 
BladderCancer_Investigation 
0 
1 
1 
1 
1 
BladderCancer_PalliativeCare 
0 
1 
1 
1 
1 
BladderCancer_Treatment 
0 
1 
1 
1 
1 
BreastCancer_Investigation 
0 
1 
1 
1 
1 
BreastCancer_PalliativeCare 
0 
1 
1 
1 
1 
Only first 10 rows of 87 are shown.
Naive
Treatment 
Priority 
FT_if_5orUnder 
FT_if_pregnant 
FT_if_tbdiagnosed 
FT_if_Hivdiagnosed 

FirstAttendance_SpuriousEmergencyCare 
1 
0 
1 
1 
1 
Alri_Pneumonia_Treatment_Outpatient 
2 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient 
2 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient_Followup 
2 
1 
1 
1 
1 
BladderCancer_Investigation 
2 
1 
1 
1 
1 
BladderCancer_PalliativeCare 
2 
1 
1 
1 
1 
BladderCancer_Treatment 
2 
1 
1 
1 
1 
BreastCancer_Investigation 
2 
1 
1 
1 
1 
BreastCancer_PalliativeCare 
2 
1 
1 
1 
1 
Only first 10 rows of 87 are shown.
Test Mode 1
Treatment 
Priority 
FT_if_5orUnder 
FT_if_pregnant 
FT_if_tbdiagnosed 
FT_if_Hivdiagnosed 

FirstAttendance_SpuriousEmergencyCare 
4 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Outpatient 
0 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient 
4 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient_Followup 
0 
1 
1 
1 
1 
BladderCancer_Investigation 
4 
1 
1 
1 
1 
BladderCancer_PalliativeCare 
0 
1 
1 
1 
1 
BladderCancer_Treatment 
4 
1 
1 
1 
1 
BreastCancer_Investigation 
0 
1 
1 
1 
1 
BreastCancer_PalliativeCare 
4 
1 
1 
1 
1 
Only first 10 rows of 87 are shown.
ClinicallyVulnerable
Treatment 
Priority 
FT_if_5orUnder 
FT_if_pregnant 
FT_if_tbdiagnosed 
FT_if_Hivdiagnosed 

FirstAttendance_SpuriousEmergencyCare 
1 
0 
1 
1 
1 
Alri_Pneumonia_Treatment_Outpatient 
3 
2 
2 
2 
2 
Alri_Pneumonia_Treatment_Inpatient 
3 
2 
2 
2 
2 
Alri_Pneumonia_Treatment_Inpatient_Followup 
3 
2 
2 
2 
2 
BladderCancer_Investigation 
3 
2 
2 
2 
2 
BladderCancer_PalliativeCare 
3 
2 
2 
2 
2 
BladderCancer_Treatment 
3 
2 
2 
2 
2 
BreastCancer_Investigation 
3 
2 
2 
2 
2 
BreastCancer_PalliativeCare 
3 
2 
2 
2 
2 
Only first 10 rows of 87 are shown.
VerticalProgrammes
Treatment 
Priority 
FT_if_5orUnder 
FT_if_pregnant 
FT_if_tbdiagnosed 
FT_if_Hivdiagnosed 

FirstAttendance_SpuriousEmergencyCare 
1 
0 
1 
1 
1 
Alri_Pneumonia_Treatment_Outpatient 
3 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient 
3 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient_Followup 
3 
1 
1 
1 
1 
BladderCancer_Investigation 
3 
1 
1 
1 
1 
BladderCancer_PalliativeCare 
3 
1 
1 
1 
1 
BladderCancer_Treatment 
3 
1 
1 
1 
1 
BreastCancer_Investigation 
3 
1 
1 
1 
1 
BreastCancer_PalliativeCare 
3 
1 
1 
1 
1 
Only first 10 rows of 87 are shown.
RMNCH
Treatment 
Priority 
FT_if_5orUnder 
FT_if_pregnant 
FT_if_tbdiagnosed 
FT_if_Hivdiagnosed 

FirstAttendance_SpuriousEmergencyCare 
1 
0 
1 
1 
1 
Alri_Pneumonia_Treatment_Outpatient 
5 
3 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient 
5 
3 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient_Followup 
5 
3 
1 
1 
1 
BladderCancer_Investigation 
5 
1 
1 
1 
1 
BladderCancer_PalliativeCare 
5 
1 
1 
1 
1 
BladderCancer_Treatment 
5 
1 
1 
1 
1 
BreastCancer_Investigation 
5 
1 
1 
1 
1 
BreastCancer_PalliativeCare 
5 
1 
1 
1 
1 
Only first 10 rows of 87 are shown.
EHP_III
Treatment 
Priority 
FT_if_5orUnder 
FT_if_pregnant 
FT_if_tbdiagnosed 
FT_if_Hivdiagnosed 

FirstAttendance_SpuriousEmergencyCare 
1 
0 
1 
1 
1 
Alri_Pneumonia_Treatment_Outpatient 
2 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient 
2 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient_Followup 
2 
1 
1 
1 
1 
BladderCancer_Investigation 
4 
1 
1 
1 
1 
BladderCancer_PalliativeCare 
4 
1 
1 
1 
1 
BladderCancer_Treatment 
4 
1 
1 
1 
1 
BreastCancer_Investigation 
4 
1 
1 
1 
1 
BreastCancer_PalliativeCare 
4 
1 
1 
1 
1 
Only first 10 rows of 87 are shown.
LCOA_EHP
Treatment 
Priority 
FT_if_5orUnder 
FT_if_pregnant 
FT_if_tbdiagnosed 
FT_if_Hivdiagnosed 

FirstAttendance_SpuriousEmergencyCare 
1 
0 
1 
1 
1 
Alri_Pneumonia_Treatment_Outpatient 
2 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient 
3 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient_Followup 
3 
1 
1 
1 
1 
BladderCancer_Investigation 
4 
1 
1 
1 
1 
BladderCancer_PalliativeCare 
4 
1 
1 
1 
1 
BladderCancer_Treatment 
4 
1 
1 
1 
1 
BreastCancer_Investigation 
4 
1 
1 
1 
1 
BreastCancer_PalliativeCare 
4 
1 
1 
1 
1 
Only first 10 rows of 87 are shown.
CVD
Treatment 
Priority 
FT_if_5orUnder 
FT_if_pregnant 
FT_if_tbdiagnosed 
FT_if_Hivdiagnosed 

FirstAttendance_SpuriousEmergencyCare 
1 
0 
1 
1 
1 
Alri_Pneumonia_Treatment_Outpatient 
3 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient 
3 
1 
1 
1 
1 
Alri_Pneumonia_Treatment_Inpatient_Followup 
3 
1 
1 
1 
1 
BladderCancer_Investigation 
3 
1 
1 
1 
1 
BladderCancer_PalliativeCare 
3 
1 
1 
1 
1 
BladderCancer_Treatment 
3 
1 
1 
1 
1 
BreastCancer_Investigation 
3 
1 
1 
1 
1 
BreastCancer_PalliativeCare 
3 
1 
1 
1 
1 
Only first 10 rows of 87 are shown.
HR_scaling_by_level_and_officer_type_table
default
Officer_Category 
L0_factor 
L1a_factor 
L1b_factor 
L2_factor 
L3_factor 
L4_factor 
L5_factor 

Clinical 
1 
1 
1 
1 
1 
1 
1 
DCSA 
1 
1 
1 
1 
1 
1 
1 
Dental 
1 
1 
1 
1 
1 
1 
1 
Laboratory 
1 
1 
1 
1 
1 
1 
1 
Mental 
1 
1 
1 
1 
1 
1 
1 
Nursing_and_Midwifery 
1 
1 
1 
1 
1 
1 
1 
Nutrition 
1 
1 
1 
1 
1 
1 
1 
Pharmacy 
1 
1 
1 
1 
1 
1 
1 
Radiography 
1 
1 
1 
1 
1 
1 
1 
data
Officer_Category 
L0_factor 
L1a_factor 
L1b_factor 
L2_factor 
L3_factor 
L4_factor 
L5_factor 

Clinical 
1 
0.795927 
0.836783 
1.00678 
1 
1 
1 
DCSA 
2.13327 
1 
1 
1 
1 
1 
1 
Dental 
1 
1.46777 
1.46777 
1.46777 
1 
1 
1 
Laboratory 
1 
1.0149 
0.997807 
1.14721 
1 
1 
1 
Mental 
1 
1 
1 
1 
1 
1 
1 
Nursing_and_Midwifery 
1 
0.605695 
0.615689 
0.799333 
1 
1 
1 
Nutrition 
1 
1 
1 
1 
1 
1 
1 
Pharmacy 
1 
1.02347 
1.06089 
1.30115 
1 
1 
1 
Radiography 
1 
1 
0.275236 
0.277971 
1 
1 
1 
custom
Officer_Category 
L0_factor 
L1a_factor 
L1b_factor 
L2_factor 
L3_factor 
L4_factor 
L5_factor 

Clinical 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
DCSA 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
Dental 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
Laboratory 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
Mental 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
Nursing_and_Midwifery 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
Nutrition 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
Pharmacy 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
Radiography 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
0.5 
x2_fac0&1
Officer_Category 
L0_factor 
L1a_factor 
L1b_factor 
L2_factor 
L3_factor 
L4_factor 
L5_factor 

Clinical 
2 
2 
2 
1 
1 
1 
1 
DCSA 
2 
2 
2 
1 
1 
1 
1 
Dental 
2 
2 
2 
1 
1 
1 
1 
Laboratory 
2 
2 
2 
1 
1 
1 
1 
Mental 
2 
2 
2 
1 
1 
1 
1 
Nursing_and_Midwifery 
2 
2 
2 
1 
1 
1 
1 
Nutrition 
2 
2 
2 
1 
1 
1 
1 
Pharmacy 
2 
2 
2 
1 
1 
1 
1 
Radiography 
2 
2 
2 
1 
1 
1 
1 
HR_scaling_by_district_table
default
District 
Factor 

Blantyre 
1 
Blantyre City 
1 
Chikwawa 
1 
Chiradzulu 
1 
Chitipa 
1 
Dedza 
1 
Dowa 
1 
Karonga 
1 
Kasungu 
1 
Only first 10 rows of 32 are shown.
yearly_HR_scaling
no_scaling
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
scaling_by_population_growth
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2019 
1 
True 
GDP_growth
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2019 
1.042 
False 
GDP_growth_fHE_case1
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2019 
1.01074 
False 
GDP_growth_fHE_case2
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2019 
1.02116 
False 
GDP_growth_fHE_case3
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2019 
1.02637 
False 
GDP_growth_fHE_case4
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2019 
1.05763 
False 
GDP_growth_fHE_case5
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2019 
1.06284 
False 
GDP_growth_fHE_case6
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2019 
1.07326 
False 
GDP_growth_FL_case1_const_tot_i
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2018 
1.1 
False 
2019 
1.042 
False 
2032 
0.861157 
False 
2033 
1.042 
False 
GDP_growth_FL_case2_const_tot_i
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2018 
1.3 
False 
2019 
1.042 
False 
2031 
0.616568 
False 
2032 
1.042 
False 
GDP_growth_FL_case1_vary_tot_in
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2018 
1.1 
False 
2019 
1.042 
False 
GDP_growth_FL_case2_vary_tot_in
year 
dynamic_HR_scaling_factor 
scale_HR_by_popsize 

2010 
1 
False 
2018 
1.3 
False 
2019 
1.042 
False 
Hiv
Name 
Description 
Type 
Value 

time_inf 
prob of time since infection for baseline adult pop 
Dataframe 

art_coverage 
coverage of ART at baseline 
Dataframe 

treatment_cascade 
spectrum estimates of treatment cascade 
Dataframe 

beta 
Transmission rate 
Real 
0.14379 
unaids_prevalence_adjustment_factor 
adjustment for baseline agespecific prevalence values to give correct population prevalence 
Real 
1.1 
prob_mtct_untreated 
Probability of mother to child transmission 
Real 
0.22 
prob_mtct_treated 
Probability of mother to child transmission, mother on ART 
Real 
0.0 
prob_mtct_incident_preg 
Probability of mother to child transmission, mother infected during pregnancy 
Real 
0.3 
monthly_prob_mtct_bf_untreated 
Probability of mother to child transmission during breastfeeding 
Real 
0.01 
monthly_prob_mtct_bf_treated 
Probability of mother to child transmission, mother infected during breastfeeding 
Real 
0.0 
rr_fsw 
Relative risk of HIV with female sex work 
Real 
25.0 
rr_circumcision 
Relative risk of HIV with circumcision 
Real 
0.4 
rr_rural 
Relative risk of HIV in rural location 
Real 
0.52 
rr_windex_poorer 
Relative risk of HIV with wealth level poorer 
Real 
0.96 
rr_windex_middle 
Relative risk of HIV with wealth level middle 
Real 
1.18 
rr_windex_richer 
Relative risk of HIV with wealth level richer 
Real 
1.19 
rr_windex_richest 
Relative risk of HIV with wealth level richest 
Real 
1.56 
rr_sex_f 
Relative risk of HIV if female 
Real 
1.43 
rr_edlevel_primary 
Relative risk of HIV with primary education 
Real 
1.18 
rr_edlevel_secondary 
Relative risk of HIV with secondary education 
Real 
1.15 
rr_edlevel_higher 
Relative risk of HIV with higher education 
Real 
1.0 
rr_schisto 
Relative risk of HIV with high intensity S. haematobium infection 
Real 
2.3 
rr_behaviour_change 
Relative risk of HIV with behaviour modification 
Real 
0.75 
proportion_reduction_in_risk_of_hiv_aq_if_on_prep 
Proportion reduction in risk of HIV acquisition if on PrEP. 0 for no efficacy; 1.0 for perfect efficacy. 
Real 
0.9 
mean_months_between_aids_and_death 
Mean number of months (distributed exponentially) for the time between AIDS and AIDS Death 
Real 
18.0 
mean_months_between_aids_and_death_infant 
Mean number of months for the time between AIDS and AIDS Death for infants 
Real 
6.0 
infection_to_death_weibull_shape_1519 
Shape parameter for Weibull describing time between infection and death for 1519 yo (units: years) 
Real 
2.0 
infection_to_death_weibull_shape_2024 
Shape parameter for Weibull describing time between infection and death for 2024 yo (units: years) 
Real 
2.0 
infection_to_death_weibull_shape_2529 
Shape parameter for Weibull describing time between infection and death for 2529 yo (units: years) 
Real 
2.0 
infection_to_death_weibull_shape_3034 
Shape parameter for Weibull describing time between infection and death for 3034 yo (units: years) 
Real 
2.0 
infection_to_death_weibull_shape_3539 
Shape parameter for Weibull describing time between infection and death for 3539 yo (units: years) 
Real 
2.0 
infection_to_death_weibull_shape_4044 
Shape parameter for Weibull describing time between infection and death for 4044 yo (units: years) 
Real 
2.0 
infection_to_death_weibull_shape_4549 
Shape parameter for Weibull describing time between infection and death for 4549 yo (units: years) 
Real 
2.0 
infection_to_death_weibull_scale_1519 
Scale parameter for Weibull describing time between infection and death for 1519 yo (units: years) 
Real 
16.0 
infection_to_death_weibull_scale_2024 
Scale parameter for Weibull describing time between infection and death for 2024 yo (units: years) 
Real 
15.4 
infection_to_death_weibull_scale_2529 
Scale parameter for Weibull describing time between infection and death for 2529 yo (units: years) 
Real 
14.1 
infection_to_death_weibull_scale_3034 
Scale parameter for Weibull describing time between infection and death for 3034 yo (units: years) 
Real 
12.1 
infection_to_death_weibull_scale_3539 
Scale parameter for Weibull describing time between infection and death for 3539 yo (units: years) 
Real 
11.0 
infection_to_death_weibull_scale_4044 
Scale parameter for Weibull describing time between infection and death for 4044 yo (units: years) 
Real 
10.01 
infection_to_death_weibull_scale_4549 
Scale parameter for Weibull describing time between infection and death for 4549 yo (units: years) 
Real 
7.9 
art_default_to_aids_mean_years 
Mean years between when a person (any change) stops being on treatment to when AIDS is onset (if the absence of resuming treatment). 
Real 
5.0 
prop_delayed_aids_onset 
Proportion of PLHIV that will have delayed AIDS onset to compensate for AIDSTB 
Real 
0.3 
mean_survival_for_infants_infected_prior_to_birth 
Exponential rate parameter for mortality in infants who are infected before birth 
Real 
1.08 
infection_to_death_infant_infection_after_birth_weibull_scale 
Weibull scale parameter for mortality in infants who are infected after birth 
Real 
16.0 
infection_to_death_infant_infection_after_birth_weibull_shape 
Weibull shape parameter for mortality in infants who are infected after birth 
Real 
2.7 
hiv_testing_rates 
annual rates of testing for children and adults 
Dataframe 

rr_test_hiv_positive 
relative likelihood of having HIV test for people with HIV 
Real 
1.1 
hiv_testing_rate_adjustment 
adjustment to current testing rates to account for multiple routes into HIV testing 
Real 
0.75 
treatment_initiation_adjustment 
adjustment to current ART coverage levels to account for defaulters 
Real 
1.0 
vs_adjustment 
adjustment to current viral suppression levels to account for defaulters 
Real 
1.0 
prob_hiv_test_at_anc_or_delivery 
probability of a women having hiv test at anc or following delivery 
Real 
0.95 
prob_hiv_test_for_newborn_infant 
probability of a newborn infant having HIV test predischarge 
Real 
0.95 
prob_start_art_or_vs 
Probability that a person will start treatment and be virally suppressed following testing 
Dataframe 

prob_behav_chg_after_hiv_test 
Probability that a person will change risk behaviours, if HIVnegative, following testing 
Real 
0.5 
prob_prep_for_fsw_after_hiv_test 
Probability that a FSW will start PrEP, if HIVnegative, following testing 
Real 
0.05 
prob_prep_for_agyw 
Probability that adolescent girls / young women will start PrEP 
Real 
0.0 
prob_circ_after_hiv_test 
Probability that a male will be circumcised, if HIVnegative, following testing 
Real 
0.05 
prob_circ_for_child_before_2020 
Probability that a male aging <15 yrs will be circumcised before year 2020 
Real 
0.0128 
prob_circ_for_child_from_2020 
Probability that a male aging <15 yrs will be circumcised from year 2020, which is different from before 2020 as children vmmc policy/fund/cases has changed, according to PEPFAR 2020 Country Operational Plan and DHIS2 data 
Real 
0.0008 
probability_of_being_retained_on_prep_every_3_months 
Probability that someone who has initiated on prep will attend an appointment and be on prep for the next 3 months, until the next appointment. 
Real 
0.5 
probability_of_being_retained_on_art_every_3_months 
Probability that someone who has initiated on treatment will attend an appointment and be on treatment for next 3 months, until the next appointment. 
Real 
0.95 
probability_of_seeking_further_art_appointment_if_drug_not_available 
Probability that a person who ‘should’ be on art will seek another appointment (the following day and try for each of the next 7 days) if drugs were not available. 
Real 
0.9 
probability_of_seeking_further_art_appointment_if_appointment_not_available 
Probability that a person who ‘should’ be on art will seek another appointment if the healthsystem has not been able to provide them with an appointment 
Real 
0.9 
prep_start_year 
Year from which PrEP is available 
Real 
2018.0 
ART_age_cutoff_young_child 
Age cutoff for ART regimen for young children 
Integer 
1 
ART_age_cutoff_older_child 
Age cutoff for ART regimen for older children 
Integer 
10 
rel_probability_art_baseline_aids 
relative probability of person with HIV infection over 10 years being on ART at baseline 
Real 
10.0 
aids_tb_treatment_adjustment 
probability of death if aids and tb, person on treatment for tb 
Real 
0.5 
hiv_healthseekingbehaviour_cap 
number of repeat visits assumed for healthcare services 
Integer 
5 
dispensation_period_months 
length of prescription for ARVs in months, same for all PLHIV 
Real 
3.0 
length_of_inpatient_stay_if_terminal 
length in days of inpatient stay for endoflife HIV patients: list has two elements [lowboundinclusive, highboundexclusive] 
List 
[14, 20] 
type_of_scaleup 
argument to determine type scaleup of program which will be implemented, can be ‘none’, ‘target’ or ‘max’ 
String 
none 
scaleup_start_year 
the year when the scaleup starts (it will occur on 1st January of that year) 
Integer 
2025 
scaleup_parameters 
the parameters and values changed in scenario analysis 
Dataframe 
time_inf
year 
probability_infection 
scaled_prob 
Unnamed: 3 
Unnamed: 4 
Unnamed: 5 
Distribution by CD4 count  HIV+ not on ART (15+)  (Male+Female) 
Unnamed: 7 
Unnamed: 8 
Unnamed: 9 
Unnamed: 10 
Unnamed: 11 
Unnamed: 12 
Unnamed: 13 
Unnamed: 14 
Unnamed: 15 
Unnamed: 16 

20 
0.0145011 
0.0167087 
nan 
nan 
nan 
malawi_2021_v14_aim_v6.07 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
19 
0.018403 
0.0212047 
nan 
nan 
nan 
2010 
150189.14229 
134383.22199 
114415.4995 
52950.4893 
77739.93484 
28957.76557 
20245.60225 
578882 
276528 
0.350438 
18 
0.022511 
0.0259382 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
17 
0.0264052 
0.0304252 
nan 
nan 
nan 
Distribution by CD4 count  HIV+ on ART (15+)  (Male+Female) 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
16 
0.0305511 
0.0352023 
nan 
nan 
nan 
nan 
> 500 
350  500 
250  349 
200  249 
100  199 
50  99 
< 50 
nan 
nan 
nan 
15 
0.0338398 
0.0389916 
nan 
nan 
nan 
malawi_2021_v14_aim_v6.07 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
14 
0.0383583 
0.044198 
nan 
nan 
nan 
2010 
6268.17276 
5523.92113 
4618.85403 
44214.79861 
77016.22359 
36469.29667 
36098.98313 
210210 
nan 
nan 
13 
0.0423454 
0.0487921 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
12 
0.0452294 
0.0521152 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
nan 
Only first 10 rows of 21 are shown.
art_coverage
year 
age 
single_age 
sex 
art_coverage 
prop_coverage 

2009 
0_4 
1 
F 
10.69 
0.1069 
2009 
0_4 
2 
F 
10.69 
0.1069 
2009 
0_4 
3 
F 
10.69 
0.1069 
2009 
0_4 
4 
F 
10.69 
0.1069 
2009 
5_9 
5 
F 
7.6 
0.076 
2009 
5_9 
6 
F 
7.6 
0.076 
2009 
5_9 
7 
F 
7.6 
0.076 
2009 
5_9 
8 
F 
7.6 
0.076 
2009 
5_9 
9 
F 
7.6 
0.076 
Only first 10 rows of 1662 are shown.
treatment_cascade
year 
age 
plhiv 
know_status 
on_art 
plhiv_virally_suppressed 
prob_art_if_dx 
virally_suppressed_on_art 
vs_assumed_value 

2011 
adults 
100 
73.2277 
37.6375 
nan 
0.513979 
80 
yes 
2012 
adults 
100 
76.423 
46.3159 
42.1013 
0.606046 
91 
no 
2013 
adults 
100 
78.7843 
52.9497 
47.6735 
0.672084 
90 
no 
2014 
adults 
100 
80.8733 
59.2378 
51.5664 
0.732477 
87 
no 
2015 
adults 
100 
82.7952 
64.1071 
57.269 
0.774285 
89 
no 
2016 
adults 
100 
85.3839 
71.6873 
65.3256 
0.839588 
91 
no 
2017 
adults 
100 
88.3281 
78.056 
69.322 
0.883705 
89 
no 
2018 
adults 
100 
90.6581 
84.2257 
76.8029 
0.929047 
91 
no 
2019 
adults 
100 
92.1484 
85.4227 
79.9867 
0.927012 
94 
no 
Only first 10 rows of 32 are shown.
hiv_testing_rates
year 
adults_15plus 
children0_14 
total 
pop_size_children0_14 
pop_size_adults15plus 
annual_testing_rate_children 
annual_testing_rate_adults 
annual_testing_rate_all_ages 
testing_yield 

2011 
1.47766e+06 
147536 
1.62766e+06 
6.84823e+06 
8.2137e+06 
0.0215437 
0.179902 
0.108065 
nan 
2012 
1.54915e+06 
149514 
1.70682e+06 
6.94965e+06 
8.51109e+06 
0.0215139 
0.182016 
0.110397 
nan 
2013 
1.56574e+06 
136888 
1.70263e+06 
7.04596e+06 
8.8196e+06 
0.0194279 
0.177529 
0.107316 
nan 
2014 
1.73309e+06 
161964 
1.89506e+06 
7.13959e+06 
9.13714e+06 
0.0226853 
0.189676 
0.116427 
nan 
2015 
2.01048e+06 
215807 
2.22629e+06 
7.23293e+06 
9.46126e+06 
0.0298367 
0.212496 
0.133357 
nan 
2016 
2.91753e+06 
483515 
3.40104e+06 
7.32839e+06 
9.79171e+06 
0.0659783 
0.297959 
0.198658 
nan 
2017 
3.62603e+06 
539283 
4.16531e+06 
7.42836e+06 
1.01303e+07 
0.0725978 
0.35794 
0.237223 
0.023 
2018 
4.09092e+06 
544240 
4.63516e+06 
7.53526e+06 
1.04771e+07 
0.0722257 
0.390464 
0.257332 
0.01925 
2019 
3.64886e+06 
418104 
4.06697e+06 
7.66667e+06 
1.09056e+07 
0.0545353 
0.334586 
0.218981 
0.01425 
Only first 10 rows of 41 are shown.
prob_start_art_or_vs
year 
age 
plhiv 
know_status 
on_art 
plhiv_virally_suppressed 
prob_art_if_dx 
virally_suppressed_on_art 
vs_assumed_value 

2011 
adults 
100 
73.2277 
37.6375 
nan 
0.513979 
80 
yes 
2012 
adults 
100 
76.423 
46.3159 
42.1013 
0.606046 
91 
no 
2013 
adults 
100 
78.7843 
52.9497 
47.6735 
0.672084 
90 
no 
2014 
adults 
100 
80.8733 
59.2378 
51.5664 
0.732477 
87 
no 
2015 
adults 
100 
82.7952 
64.1071 
57.269 
0.774285 
89 
no 
2016 
adults 
100 
85.3839 
71.6873 
65.3256 
0.839588 
91 
no 
2017 
adults 
100 
88.3281 
78.056 
69.322 
0.883705 
89 
no 
2018 
adults 
100 
90.6581 
84.2257 
76.8029 
0.929047 
91 
no 
2019 
adults 
100 
92.1484 
85.4227 
79.9867 
0.927012 
94 
no 
Only first 10 rows of 32 are shown.
scaleup_parameters
parameter 
target_value 
min_value 
max_value 

reduction_in_hiv_beta 
0.9 
1 
0 
prob_prep_for_fsw_after_hiv_test 
0.5 
0 
1 
prob_prep_for_agyw 
0.1 
0 
1 
probability_of_being_retained_on_prep_every_3_months 
0.75 
0 
1 
probability_of_being_retained_on_art_every_3_months 
1 
0 
1 
prob_circ_after_hiv_test 
0.25 
0 
1 
annual_testing_rate_adults 
0.4 
0 
1 
prob_hiv_test_at_anc_or_delivery 
0.95 
0 
1 
prob_hiv_test_for_newborn_infant 
0.95 
0 
1 
virally_suppressed_on_art 
95 
0 
100 
Labour
Name 
Description 
Type 
Value 

intercept_parity_lr2010 
intercept value for linear regression equation predicating womens parity at 2010 baseline 
List 
[2.81, 2.81] 
effect_age_parity_lr2010 
effect of an increase in age by 1 year in the linear regression equation predicating womens parity at 2010 baseline 
List 
[0.21, 0.21] 
effect_mar_stat_2_parity_lr2010 
effect of a change in marriage status from comparison (level 1) in the linear regression equation predicating womans parity at 2010 baseline 
List 
[0.84, 0.84] 
effect_mar_stat_3_parity_lr2010 
effect of a change in marriage status from comparison (level 1) in the linear regression equation predicating womans parity at 2010 baseline 
List 
[0.14, 0.14] 
effect_wealth_lev_4_parity_lr2010 
effect of an increase in wealth level in the linear regression equation predicating womans parity at 2010 base line 
List 
[0.09, 0.09] 
effect_wealth_lev_3_parity_lr2010 
effect of an increase in wealth level in the linear regression equation predicating womans parity at 2010 base line 
List 
[0.18, 0.18] 
effect_wealth_lev_2_parity_lr2010 
effect of an increase in wealth level in the linear regression equation predicating womans parity at 2010 base line 
List 
[0.22, 0.22] 
effect_wealth_lev_1_parity_lr2010 
effect of an increase in wealth level in the linear regression equation predicating womans parity at 2010 base line 
List 
[0.48, 0.48] 
effect_edu_lev_2_parity_lr2010 
effect of an increase in education level in the linear regression equation predicating womans parity at 2010 base line 
List 
[0.33, 0.33] 
effect_edu_lev_3_parity_lr2010 
effect of an increase in education level in the linear regression equation predicating womans parity at 2010 base line 
List 
[1, 1] 
effect_rural_parity_lr2010 
effect of rural living in the linear regression equation predicating womans parity at 2010 base line 
List 
[0.19, 0.19] 
prob_previous_caesarean_at_baseline 
probability of previously having delivered via caesarean section at baseline 
List 
[0.046, 0.046] 
risk_post_term_labour 
risk of remaining pregnant past 42 weeks 
List 
[0.077, 0.077] 
rr_potl_bmi_30_35 
effect of maternal BMI being between 30 and 35 on risk of post term labour 
List 
[1.42, 1.42] 
rr_potl_bmi_35+ 
effect of maternal BMI being between above 35 on risk of post term labour 
List 
[1.55, 1.55] 
list_limits_for_defining_term_status 
List of number of days of gestation used to define term, early preterm, late preterm and post term delivery 
List 
[[259, 293, 148, 230, 231, 258, 294], [259, 293, 148, 230, 231, 258, 294]] 
allowed_interventions 
list of interventions allowed to run, used in analysis 
List 
[[‘prophylactic_labour_interventions’, ‘assessment_and_treatment_of_severe_pre_eclampsia’, ‘assessment_and_treatment_of_obstructed_labour’, ‘assessment_and_treatment_of_maternal_sepsis’, ‘assessment_and_treatment_of_hypertension’, ‘assessment_and_treatment_of_eclampsia’, ‘assessment_and_plan_for_referral_antepartum_haemorrhage’, ‘assessment_and_plan_for_referral_uterine_rupture’, ‘active_management_of_the_third_stage_of_labour’, ‘assessment_and_treatment_of_pph_retained_placenta’, ‘assessment_and_treatment_of_pph_uterine_atony’], [‘prophylactic_labour_interventions’, ‘assessment_and_treatment_of_severe_pre_eclampsia’, ‘assessment_and_treatment_of_obstructed_labour’, ‘assessment_and_treatment_of_maternal_sepsis’, ‘assessment_and_treatment_of_hypertension’, ‘assessment_and_treatment_of_eclampsia’, ‘assessment_and_plan_for_referral_antepartum_haemorrhage’, ‘assessment_and_plan_for_referral_uterine_rupture’, ‘active_management_of_the_third_stage_of_labour’, ‘assessment_and_treatment_of_pph_retained_placenta’, ‘assessment_and_treatment_of_pph_uterine_atony’]] 
mean_birth_weights 
list of mean birth weights from gestational age at birth 2441 weeks 
List 
[[657, 746, 851, 966, 1096, 1240, 1440, 1641, 1841, 2041, 2242, 2442, 2736, 2856, 2995, 3036, 3117, 3136], [657, 746, 851, 966, 1096, 1240, 1440, 1641, 1841, 2041, 2242, 2442, 2736, 2856, 2995, 3036, 3117, 3136]] 
standard_deviation_birth_weights 
list of standard deviations associated with mean birth weights from gestational age at birth 2441 weeks 
List 
[[113, 140, 169, 196, 218, 235, 274, 312, 351, 390, 428, 460, 467, 398, 356, 351, 396, 351], [113, 140, 169, 196, 218, 235, 274, 312, 351, 390, 428, 460, 467, 398, 356, 351, 396, 351]] 
residual_prob_of_macrosomia 
probability that those allocated to be normal birth weight and above will be macrosomic (>4kg) 
List 
[0.057, 0.057] 
prob_obstruction_cpd 
risk of a woman developing obstructed labour secondary to cephalopelvic disproportion 
List 
[0.012, 0.022] 
rr_obstruction_cpd_stunted_mother 
relative risk of obstruction secondary to CPD in mothers who are stunted 
List 
[2.4, 2.4] 
rr_obstruction_foetal_macrosomia 
relative risk of obstruction secondary to CPD in mothers who are carrying a macrosomic foetus 
List 
[3.3, 3.3] 
prob_obstruction_malpos_malpres 
risk of a woman developing obstructed labour secondary to malposition or malpresentation 
List 
[0.005, 0.009] 
prob_obstruction_other 
risk of a woman developing obstructed labour secondary to other causes 
List 
[0.0015, 0.0027] 
prob_placental_abruption_during_labour 
probability of a woman developing placental abruption during labour 
List 
[0.0005, 0.0005] 
prob_aph_placenta_praevia_labour 
probability of a woman with placenta praevia experiencing an APH during labour 
List 
[0.25, 0.25] 
prob_aph_placental_abruption_labour 
probability of a woman with placental abruption experiencing an APH during labour 
List 
[0.9, 0.9] 
rr_placental_abruption_hypertension 
Relative risk of placental abruption in women with hypertension 
List 
[2.2, 2.2] 
rr_placental_abruption_previous_cs 
Relative risk of placental abruption in women who delivered previously via caesarean section 
List 
[1.3, 1.3] 
severity_maternal_haemorrhage 
probability a maternal hemorrhage is nonsevere (<1000mls) or severe (>1000mls) 
List 
[[0.8, 0.2], [0.8, 0.2]] 
cfr_aph 
case fatality rate for antepartum haemorrhage during labour 
List 
[0.11, 0.04] 
prob_sepsis_chorioamnionitis 
risk of sepsis following chorioamnionitis infection 
List 
[0.0002, 0.00018] 
rr_sepsis_chorio_prom 
relative risk of chorioamnionitis following PROM 
List 
[1.76, 1.76] 
prob_sepsis_endometritis 
risk of sepsis following endometritis 
List 
[6.9e05, 6.2e05] 
rr_sepsis_endometritis_post_cs 
relative risk of endometritis following caesarean delivery 
List 
[12.1, 12.1] 
prob_sepsis_urinary_tract 
risk of sepsis following urinary tract infection 
List 
[5.4e05, 5.4e05] 
prob_sepsis_skin_soft_tissue 
risk of sepsis following skin or soft tissue infection 
List 
[3.9e05, 3.5e05] 
rr_sepsis_sst_post_cs 
relative risk of skin/soft tissue sepsis following caesarean delivery 
List 
[3.9, 3.9] 
cfr_sepsis 
case fatality rate for sepsis during labour 
List 
[0.75, 0.49] 
cfr_pp_sepsis 
case fatality rate for sepsis following delivery 
List 
[0.75, 0.49] 
prob_uterine_rupture 
probability of a uterine rupture during labour 
List 
[0.0011, 0.0005] 
rr_ur_parity_2 
relative risk of uterine rupture in women who have delivered 2 times previously 
List 
[2.74, 2.74] 
rr_ur_parity_3_or_4 
relative risk of uterine rupture in women who have delivered 34 times previously 
List 
[4.89, 4.89] 
rr_ur_parity_5+ 
relative risk of uterine rupture in women who have delivered > 5 times previously 
List 
[7.57, 7.57] 
rr_ur_prev_cs 
relative risk of uterine rupture in women who have previously delivered via caesarean section 
List 
[2.02, 2.02] 
rr_ur_obstructed_labour 
relative risk of uterine rupture in women who have been in obstructed labour 
List 
[23.6, 23.6] 
cfr_uterine_rupture 
case fatality rate for uterine rupture in labour 
List 
[0.65, 0.5] 
prob_progression_gest_htn 
probability of gestational hypertension progressing to severe gestational hypertensionduring/after labour 
List 
[0.036, 0.036] 
prob_progression_severe_gest_htn 
probability of severe gestational hypertension progressing to severe preeclampsia during/after labour 
List 
[0.13, 0.13] 
prob_progression_mild_pre_eclamp 
probability of mild preeclampsia progressing to severe preeclampsia during/after labour 
List 
[0.14, 0.14] 
prob_progression_severe_pre_eclamp 
probability of severe preeclampsia progressing to eclampsia during/after labour 
List 
[0.29, 0.29] 
cfr_eclampsia 
case fatality rate for eclampsia during labours 
List 
[0.028, 0.03] 
cfr_severe_pre_eclamp 
case fatality rate for severe pre eclampsia during labour 
List 
[0.018, 0.018] 
prob_ip_still_birth 
baseline probability of intrapartum still birth 
List 
[0.006, 0.005] 
rr_still_birth_maternal_death 
relative risk of still birth in mothers who have died during labour 
List 
[180, 180] 
rr_still_birth_ur 
relative risk of still birth in mothers experiencing uterine rupture 
List 
[56.6, 56.6] 
rr_still_birth_ol 
relative risk of still birth in mothers experiencing obstructed labour 
List 
[4.5, 4.5] 
rr_still_birth_aph 
relative risk of still birth in mothers experiencing antepartum haemorrhage 
List 
[2.1, 2.1] 
rr_still_birth_hypertension 
relative risk of still birth in mothers experiencing hypertension 
List 
[4.5, 4.5] 
rr_still_birth_sepsis 
relative risk of still birth in mothers experiencing intrapartum sepsis 
List 
[2, 2] 
rr_still_birth_multiple_pregnancy 
relative risk of still birth in mothers pregnant with twins 
List 
[3, 3] 
prob_both_twins_ip_still_birth 
probability that if this mother will experience still birth, and she is pregnant with twins, that neither baby will survive 
List 
[0.8, 0.8] 
prob_pph_uterine_atony 
risk of pph after experiencing uterine atony 
List 
[0.006, 0.011] 
rr_pph_ua_hypertension 
relative risk risk of pph after secondary to uterine atony in hypertensive women 
List 
[1.84, 1.84] 
rr_pph_ua_multiple_pregnancy 
relative risk risk of pph after secondary to uterine atony in women pregnant with twins 
List 
[2.16, 2.16] 
rr_pph_ua_placental_abruption 
relative risk risk of pph after secondary to uterine atony in women with placental abruption 
List 
[2.74, 2.74] 
rr_pph_ua_macrosomia 
relative risk risk of pph after secondary to uterine atony in women with macrosomic foetus 
List 
[1.46, 1.46] 
rr_pph_ua_diabetes 
risk of pph after experiencing uterine atony 
List 
[1.22, 1.22] 
prob_pph_retained_placenta 
risk of pph after experiencing retained placenta 
List 
[0.001, 0.0016] 
prob_pph_other_causes 
risk of pph after experiencing other pph causes 
List 
[0.0007, 0.001] 
cfr_pp_pph 
case fatality rate for postpartum haemorrhage 
List 
[0.22, 0.08] 
rr_death_from_haem_with_anaemia 
relative risk increase of death in women who are anaemic at time of PPH 
List 
[1.5, 1.5] 
odds_deliver_in_health_centre 
odds of a woman delivering in a health centre compared to a hospital 
List 
[0.69, 1.08] 
rrr_hc_delivery_age_20_24 
relative risk ratio for a woman aged 2024 delivering in a health centre compared to a hospital 
List 
[0.79, 1] 
rrr_hc_delivery_age_25_29 
relative risk ratio for a woman aged 2529 delivering in a health centre compared to a hospital 
List 
[0.5, 0.56] 
rrr_hc_delivery_age_30_34 
relative risk ratio for a woman aged 3034 delivering in a health centre compared to a hospital 
List 
[0.27, 0.32] 
rrr_hc_delivery_age_35_39 
relative risk ratio for a woman aged 3539 delivering in a health centre compared to a hospital 
List 
[0.13, 0.14] 
rrr_hc_delivery_age_40_44 
relative risk ratio for a woman aged 4044 delivering in a health centre compared to a hospital 
List 
[0.06, 0.07] 
rrr_hc_delivery_age_45_49 
relative risk ratio for a woman aged 4549 delivering in a health centre compared to a hospital 
List 
[0.02, 0.03] 
rrr_hc_delivery_wealth_4 
relative risk ratio of a woman at wealth level 4 delivering at health centre compared to a hospital 
List 
[0.82, 0.79] 
rrr_hc_delivery_wealth_3 
relative risk ratio of a woman at wealth level 3 delivering at health centre compared to a hospital 
List 
[0.77, 0.73] 
rrr_hc_delivery_wealth_2 
relative risk ratio of a woman at wealth level 2 delivering at health centre compared to a hospital 
List 
[0.62, 0.58] 
rrr_hc_delivery_wealth_1 
relative risk ratio of a woman at wealth level 1 delivering at health centre compared to a hospital 
List 
[0.55, 0.43] 
rrr_hc_delivery_parity_3_to_4 
relative risk ratio for a woman with a parity of 34 delivering in a health centre compared toa hospital 
List 
[2, 1.85] 
rrr_hc_delivery_parity_>4 
relative risk ratio of a woman with a parity >4 delivering in health centre compared to a hospital 
List 
[3.9, 3.8] 
rrr_hc_delivery_rural 
relative risk ratio of a married woman delivering in a health centre compared to a hospital 
List 
[1.99, 1.81] 
rrr_hc_delivery_married 
relative risk ratio of a married woman delivering in a health centre compared to a hospital 
List 
[1.3, 1.42] 
odds_deliver_at_home 
odds of a woman delivering at home compared to a hospital 
List 
[0.37, 0.09] 
rrr_hb_delivery_age_20_24 
relative risk ratio for a woman aged 2024 delivering at home compared to a hospital 
List 
[1.42, 1] 
rrr_hb_delivery_age_25_29 
relative risk ratio for a woman aged 2529 delivering at home compared to a hospital 
List 
[1, 0.58] 
rrr_hb_delivery_age_30_34 
relative risk ratio for a woman aged 3034 delivering at home compared to a hospital 
List 
[0.42, 0.25] 
rrr_hb_delivery_age_35_39 
relative risk ratio for a woman aged 3539 delivering at home compared to a hospital 
List 
[0.24, 0.16] 
rrr_hb_delivery_age_40_44 
relative risk ratio for a woman aged 4044 delivering at home compared to a hospital 
List 
[0.12, 0.07] 
rrr_hb_delivery_age_45_49 
relative risk ratio for a woman aged 4549 delivering at home compared to a hospital 
List 
[0.05, 0.04] 
rrr_hb_delivery_rural 
relative risk ratio of a rural delivering at home compared to a hospital 
List 
[1.73, 1] 
rrr_hb_delivery_primary_education 
relative risk ratio of a woman with a primary education delivering at home compared to a hospital 
List 
[0.76, 0.79] 
rrr_hb_delivery_secondary_education 
relative risk ratio of a woman with a secondary education delivering at home compared to a hospital 
List 
[0.46, 0.51] 
rrr_hb_delivery_wealth_4 
relative risk ratio of a woman at wealth level 4 delivering at home compared to a hospital 
List 
[0.82, 0.74] 
rrr_hb_delivery_wealth_3 
relative risk ratio of a woman at wealth level 3 delivering at home compared to a hospital 
List 
[0.72, 0.68] 
rrr_hb_delivery_wealth_2 
relative risk ratio of a woman at wealth level 2 delivering at home compared to a hospital 
List 
[0.41, 0.49] 
rrr_hb_delivery_wealth_1 
relative risk ratio of a woman at wealth level 1 delivering at home compared to a hospital 
List 
[0.2, 0.17] 
rrr_hb_delivery_parity_3_to_4 
relative risk ratio for a woman with a parity of 34 delivering at home compared toa hospital 
List 
[2.4, 1] 
rrr_hb_delivery_parity_>4 
relative risk ratio of a woman with a parity >4 delivering at home compared to a hospital 
List 
[5.25, 1] 
rrr_hb_delivery_married 
relative risk ratio of a married woman delivering in a home compared to a hospital 
List 
[0.63, 1] 
probability_delivery_hospital 
probability of delivering in a hospital 
List 
[0.32, 0.4] 
prob_timings_pnc 
probabilities that a woman who will receive a PNC check will receive care <48hrs post birth or > 48hrs post birth 
List 
[[0.85, 0.15], [0.88, 0.12]] 
odds_will_attend_pnc 
baseline odss a woman will seek PNC for her and her newborn following delivery 
List 
[0.9, 0.9] 
or_pnc_age_30_35 
odds ratio for women aged 3035 attending PNC 
List 
[1.75, 1.75] 
or_pnc_age_>35 
odds ratio for women aged > 35 attending PNC 
List 
[1.86, 1.86] 
or_pnc_rural 
odds ratio for women who live rurally attending PNC 
List 
[0.55, 0.55] 
or_pnc_wealth_level_1 
odds ratio for women from the highest wealth level attending PNC 
List 
[0.72, 0.72] 
or_pnc_anc4+ 
odds ratio for women who attended ANC4+ attending PNC 
List 
[1.2, 1.2] 
or_pnc_caesarean_delivery 
odds ratio for women who delivered by caesarean attending PNC 
List 
[1.93, 1.93] 
or_pnc_facility_delivery 
odds ratio for women who delivered in a health facility attending PNC 
List 
[1.91, 1.91] 
or_pnc_parity_>4 
odds ratio for women with a parity of >4 attending PNC 
List 
[0.03, 0.03] 
probs_of_attending_pn_event_by_day 
probabilities used in a weighted random draw to determine when a woman will attend the postnatal event 
List 
[[0.4, 0.3, 0.2, 0.05, 0.05], [0.4, 0.3, 0.2, 0.05, 0.05]] 
prob_careseeking_for_complication 
probability of a woman seeking skilled assistance after developing a complication at a home birth 
List 
[0.782, 0.782] 
prob_careseeking_for_complication_pn 
probability of a woman seeking skilled assistance after developing a postnatal complication following a home birth 
List 
[0.782, 0.782] 
test_care_seeking_probs 
dummy probabilities of delivery care seeking used in testing 
List 
[[0.33, 0.33, 0.34], [0.33, 0.33, 0.34]] 
prob_delivery_modes_ec 
probabilities that a woman admitted with eclampsia will deliver normally, via caesarean or via assisted vaginal delivery 
List 
[[0, 0, 1], [0, 0, 1]] 
prob_delivery_modes_spe 
probabilities that a woman admitted with severe preeclampsia will deliver normally, via caesarean or via assisted vaginal delivery 
List 
[[0.05, 0.05, 0.9], [0.05, 0.05, 0.9]] 
residual_prob_avd 
probabilities that a woman will deliver via assisted vaginal delivery for an indication not explicitly modelled 
List 
[0.128, 0.128] 
residual_prob_caesarean 
probabilities that a woman will deliver via caesarean section for an indication not explicitly modelled 
List 
[0.0188, 0.022] 
prob_adherent_ifa 
probability that a woman started on postnatal IFA will be adherent 
List 
[0.37, 0.34] 
effect_of_ifa_for_resolving_anaemia 
relative effect of iron and folic acid on anaemia status 
List 
[0.7, 0.7] 
number_ifa_tablets_required_postnatally 
total number of iron and folic acid tablets required during postnatal period 
List 
[93, 93] 
treatment_effect_maternal_infection_clean_delivery 
Effect of clean delivery practices on risk of maternal infection 
List 
[0.4, 0.4] 
treatment_effect_maternal_chorio_abx_prom 
Relative effect of antibiotics for premature rupture of membranes on maternal risk of chorioamnionitis prior to birth 
List 
[0.66, 0.66] 
treatment_effect_amtsl 
relative risk of severe postpartum haemorrhage following active management of the third stage of labour 
List 
[0.34, 0.34] 
prob_haemostatis_uterotonics 
probability of uterotonics stopping a postpartum haemorrhage due to uterine atony 
List 
[0.57, 0.57] 
prob_successful_manual_removal_placenta 
probability of manual removal of retained products arresting a post partum haemorrhage 
List 
[0.75, 0.75] 
success_rate_pph_surgery 
probability of surgery for postpartum haemorrhage being successful 
List 
[0.79, 0.79] 
pph_treatment_effect_surg_md 
effect of surgery on maternal death due to postpartum haemorrhage 
List 
[0.25, 0.25] 
pph_treatment_effect_hyst_md 
effect of hysterectomy on maternal death due to postpartum haemorrhage 
List 
[0.25, 0.25] 
pph_bt_treatment_effect_md 
effect of blood transfusion treatment for postpartum haemorrhage on risk of maternal death 
List 
[0.4, 0.4] 
sepsis_treatment_effect_md 
effect of treatment for sepsis on risk of maternal death 
List 
[0.2, 0.2] 
success_rate_uterine_repair 
probability repairing a ruptured uterus surgically 
List 
[0.83, 0.83] 
prob_successful_assisted_vaginal_delivery 
probability of successful assisted vaginal delivery 
List 
[0.7, 0.7] 
ur_repair_treatment_effect_md 
effect of surgical uterine repair treatment for uterine rupture on risk of maternal death 
List 
[0.25, 0.25] 
ur_treatment_effect_bt_md 
effect of blood transfusion treatment for uterine rupture on risk of maternal death 
List 
[0.4, 0.4] 
ur_hysterectomy_treatment_effect_md 
effect of blood hysterectomy for uterine rupture on risk of maternal death 
List 
[0.25, 0.25] 
eclampsia_treatment_effect_severe_pe 
effect of treatment for severe pre eclampsia on risk of eclampsia 
List 
[0.41, 0.41] 
eclampsia_treatment_effect_md 
effect of treatment for eclampsia on risk of maternal death 
List 
[0.4, 0.4] 
anti_htns_treatment_effect_md 
effect of IV anti hypertensive treatment on risk of death secondary to severe preeclampsia/eclampsia stillbirth 
List 
[0.5, 0.5] 
anti_htns_treatment_effect_progression 
effect of IV anti hypertensive treatment on risk of progression from mild to severe gestational hypertension 
List 
[0.49, 0.49] 
aph_bt_treatment_effect_md 
effect of blood transfusion treatment for antepartum haemorrhage on risk of maternal death 
List 
[0.4, 0.4] 
treatment_effect_blood_transfusion_anaemia 
effect of blood transfusion treatment for severe anaemia 
List 
[0.9, 0.9] 
aph_cs_treatment_effect_md 
effect of caesarean section for antepartum haemorrhage on risk of maternal death 
List 
[0.25, 0.25] 
treatment_effect_avd_still_birth 
effect of assisted vaginal delivery on risk of intrapartum still birth 
List 
[0.55, 0.55] 
treatment_effect_cs_still_birth 
effect of caesarean section delivery on risk of intrapartum still birth 
List 
[0.25, 0.25] 
prob_hcw_avail_iv_abx 
average probability that a health facility providing EmONC care has a HCW available that can delivery signal function  parenteral antibiotics 
List 
[0.99, 0.99] 
prob_hcw_avail_uterotonic 
average probability that a health facility providing EmONC care has a HCW available that can delivery signal function  parenteral uterotonics 
List 
[0.99, 0.99] 
prob_hcw_avail_anticonvulsant 
average probability that a health facility providing EmONC care has a HCW available that can delivery signal function  parenteral anticonvulsants 
List 
[0.93, 0.93] 
prob_hcw_avail_man_r_placenta 
average probability that a health facility providing EmONC care has a HCW available that can delivery signal function  manual removal of retained placenta 
List 
[0.82, 0.82] 
prob_hcw_avail_avd 
average probability that a health facility providing EmONC care has a HCW available that can delivery signal function  assisted vaginal delivery 
List 
[0.46, 0.46] 
prob_hcw_avail_blood_tran 
average probability that a health facility providing EmONC care has a HCW available that can delivery signal function  blood transfusion 
List 
[0.86, 0.86] 
prob_hcw_avail_surg 
average probability that a health facility providing EmONC care has a HCW available that can delivery signal function  obstetric surgery 
List 
[0.74, 0.74] 
prob_hcw_avail_retained_prod 
average probability that a health facility providing EmONC care has a HCW available that can delivery signal function  removal of retained products of conception 
List 
[0.49, 0.49] 
prob_hcw_avail_neo_resus 
average probability that a health facility providing EmONC care has a HCW available that can delivery signal function  neonatal resuscitation 
List 
[0.98, 0.98] 
mean_hcw_competence_hc 
mean competence of HCW at delivering EmONC care at a health centre. A draw below this level prevents intervention delivery 
List 
[[0.602, 0.602], [0.602, 0.602]] 
mean_hcw_competence_hp 
mean competence of HCW at delivering EmONC care at a hospital. A draw below this level prevents intervention delivery 
List 
[[0.662, 0.662], [0.662, 0.662]] 
prob_intervention_delivered_anaemia_assessment_pnc 
probability a woman will have their Hb levels checked during PNC given that the HSI has ran and the consumables are available (proxy for clinical quality) 
List 
[0.14, 0.18] 
analysis_year 
Year on which changes in parameters as part of analysis should be enacted (1st day, 1st month) 
Integer 
2023 
la_analysis_in_progress 
Used within the pregnancy_helper_function to signify that labour/postnatal analysis is currently being conducted 
Boolean 
False 
alternative_bemonc_availability 
parameter used in analysis to allow manipulation of coverage of BEmONC interventions 
Boolean 
False 
alternative_cemonc_availability 
parameter used in analysis to allow manipulation of coverage of CEmONC interventions 
Boolean 
False 
bemonc_availability 
set probability of BEmONC intervention being delivered during analysis 
Real 
1.0 
cemonc_availability 
set probability of CEmONC intervention being delivered during analysis 
Real 
1.0 
bemonc_cons_availability 
set probability of BEmONC consumables being available 
Real 
1.0 
cemonc_cons_availability 
set probability of CEmONC consumables being available 
Real 
1.0 
alternative_pnc_coverage 
Signals within the analysis event that an alternative level of PNC coverage has been determined following the events run 
Boolean 
False 
alternative_pnc_quality 
Signals within the analysis event that an alternative level of PNC quality has been determined following the events run 
Boolean 
False 
pnc_availability_odds 
Target odds of maternal PNC coverage when analysis is being conducted  only applied ifalternative_pnc_coverage is true 
Real 
3.0 
pnc_availability_probability 
Target probability of quality/consumables when analysis is being conducted  only applied if alternative_pnc_coverage is true 
Real 
1.0 
sba_sens_analysis_max 
Signals that max coverage of SBA is being forced for sensitivity analysis 
Boolean 
False 
pnc_sens_analysis_max 
Signals that max coverage of PNC is being forced for sensitivity analysis 
Boolean 
False 
pnc_sens_analysis_min 
Signals that min coverage of SBA is being forced for sensitivity analysis 
Boolean 
False 
Lifestyle
Name 
Description 
Type 
Value 

init_p_urban 
initial proportion urban 
Dictionary 

init_p_wealth_urban 
List of probabilities of category given urban 
List 
[0.75, 0.16, 0.05, 0.02, 0.02] 
init_p_wealth_rural 
List of probabilities of category given rural 
List 
[0.11, 0.21, 0.22, 0.23, 0.23] 
init_p_bmi_urban_m_not_high_sugar_age1529_not_tob_wealth1 
List of probabilities of bmi categories for urban men age 1529 with not high sugar, not tobacco, wealth level 1 
List 
[0.06, 0.8, 0.12, 0.01, 0.01] 
init_or_higher_bmi_f 
odds ratio higher BMI if female 
Real 
3.0 
init_or_higher_bmi_rural 
odds ratio higher BMI if rural 
Real 
0.6 
init_or_higher_bmi_high_sugar 
odds ratio higher BMI if high sugar intake 
Real 
1.1 
init_or_higher_bmi_age3049 
odds ratio higher BMI if age 3049 
Real 
1.8 
init_or_higher_bmi_agege50 
odds ratio higher BMI if age ge 50 
Real 
2.7 
init_or_higher_bmi_tob 
odds ratio higher BMI if use tobacco 
Real 
0.7 
init_or_higher_bmi_per_higher_wealth_level 
odds ratio for higher initial bmi category per higher wealth level 
Real 
0.85 
init_p_high_sugar 
initital proportion with high sugar intake 
Real 
0.4 
init_p_high_salt_urban 
initital proportion with high salt intake 
Real 
0.2 
init_or_high_salt_rural 
odds ratio high salt if rural 
Real 
1.5 
init_p_ex_alc_m 
initital proportion of men with excess alcohol use 
Real 
0.15 
init_p_ex_alc_f 
initital proportion of women with excess alcohol use 
Real 
0.01 
init_p_low_ex_urban_m 
initital proportion of men with low exercise urban 
Real 
0.32 
init_or_low_ex_rural 
odds ratio low exercise rural 
Real 
0.4 
init_or_low_ex_f 
odds ratio low exercise female 
Real 
0.6 
init_p_tob_age1519_m_wealth1 
initial proportion of 1519 year old men using tobacco, wealth level 1 
Real 
0.01 
init_or_tob_f 
odds ratio tobacco use females 
Real 
0.2 
init_or_tob_age2039_m 
odds ratio tobacco use age2039 in men 
Real 
4.0 
init_or_tob_agege40_m 
odds ratio tobacco use age40+ in men 
Real 
6.0 
init_or_tob_wealth2 
odds ratio tobacco use wealth level 2 
Real 
2.0 
init_or_tob_wealth3 
odds ratio tobacco use wealth level 3 
Real 
3.0 
init_or_tob_wealth4 
odds ratio tobacco use wealth level 4 
Real 
4.0 
init_or_tob_wealth5 
odds ratio tobacco use wealth level 5 
Real 
5.0 
init_dist_mar_stat_age1520 
proportions never, current, div_wid age 1520 baseline 
List 
[0.7, 0.3, 0] 
init_dist_mar_stat_age2030 
proportions never, current, div_wid age 2030 baseline 
List 
[0.15, 0.8, 0.05] 
init_dist_mar_stat_age3040 
proportions never, current, div_wid age 3040 baseline 
List 
[0.05, 0.7, 0.25] 
init_dist_mar_stat_age4050 
proportions never, current, div_wid age 4050 baseline 
List 
[0.03, 0.5, 0.47] 
init_dist_mar_stat_age5060 
proportions never, current, div_wid age 5060 baseline 
List 
[0.03, 0.3, 0.67] 
init_dist_mar_stat_agege60 
proportions never, current, div_wid age 60+ baseline 
List 
[0.03, 0.2, 0.77] 
init_age2030_w5_some_ed 
proportions of low wealth 2030 year olds with some education at baseline 
Real 
0.97 
init_prop_age2030_w5_some_ed_sec 
proportion of low wealth aged 2030 with some education who have secondary education at baseline 
Real 
0.1 
init_p_unimproved_sanitation_urban 
initial probability of unimproved_sanitation given urban 
Real 
0.04 
init_or_unimproved_sanitation_rural 
initial odds ratio of unimproved_sanitation if rural 
Real 
4.5 
init_p_no_clean_drinking_water_urban 
initial probability of no_clean_drinking_water given urban 
Real 
0.017 
init_or_no_clean_drinking_water_rural 
initial odds ratio of no clean drinking_water if rural 
Real 
8.6 
init_p_wood_burn_stove_urban 
initial probability of wood_burn_stove given urban 
Real 
0.257 
init_or_wood_burn_stove_rural 
initial odds ratio of wood_burn_stove if rural 
Real 
40.0 
init_p_no_access_handwashing_wealth1 
initial probability of no_access_handwashing given wealth 1 
Real 
0.478 
init_or_no_access_handwashing_per_lower_wealth 
initial odds ratio of no_access_handwashing per lower wealth level 
Real 
1.06 
init_prop_primary_edu 
proportion of starting primary education at baseline age 512 
Real 
0.5 
init_rp_some_ed_age0513 
relative prevalence of some education at baseline age 513 
Real 
1.01 
init_rp_some_ed_age1320 
relative prevalence of some education at baseline age 1320 
Real 
1.0 
init_rp_some_ed_age2030 
relative prevalence of some education at baseline age 2030 
Real 
1.0 
init_rp_some_ed_age3040 
relative prevalence of some education at baseline age 3040 
Real 
1.0 
init_rp_some_ed_age4050 
relative prevalence of some education at baseline age 4050 
Real 
0.9 
init_rp_some_ed_age5060 
relative prevalence of some education at baseline age 5060 
Real 
0.9 
init_rp_some_ed_per_higher_wealth 
relative prevalence of some education at baseline per higher wealth level 
Real 
1.005 
init_rp_some_ed_sec_age1320 
relative prevalence of secondary education age 1520 
Real 
1.0 
init_rp_some_ed_sec_age3040 
relative prevalence of secondary education age 3040 
Real 
0.8 
init_rp_some_ed_sec_age4050 
relative prevalence of secondary education age 4050 
Real 
0.6 
init_rp_some_ed_sec_age5060 
relative prevalence of secondary education age 5060 
Real 
0.4 
init_rp_some_ed_sec_agege60 
relative prevalence of secondary education age 60+ 
Real 
0.2 
init_rp_some_ed_agege60 
relative prevalence of some education at baseline age age 60+ 
Real 
0.9 
init_rp_some_ed_sec_per_higher_wealth 
relative prevalence of secondary education per higher wealth level 
Real 
1.48 
r_urban 
probability per 3 months of change from rural to urban 
Real 
0.0005 
r_rural 
probability per 3 months of change from urban to rural 
Real 
1e05 
r_higher_bmi 
probability per 3 months of increase in bmi category if rural male age1529 not using tobacoo with wealth level 1 with not high sugar intake 
Real 
0.0005 
rr_higher_bmi_urban 
probability per 3 months of increase in bmi category if 
Real 
1.5 
rr_higher_bmi_f 
rate ratio for increase in bmi category for females 
Real 
3.0 
rr_higher_bmi_age3049 
rate ratio for increase in bmi category for age 3049 
Real 
1.8 
rr_higher_bmi_agege50 
rate ratio for increase in bmi category for age ge 50 
Real 
2.7 
rr_higher_bmi_tob 
rate ratio for increase in bmi category for tobacco users 
Real 
0.7 
rr_higher_bmi_per_higher_wealth 
rate ratio for increase in bmi category per higher wealth level 
Real 
0.85 
rr_higher_bmi_high_sugar 
rate ratio for increase in bmi category for high sugar intake 
Real 
1.2 
r_lower_bmi 
probability per 3 months of decrease in bmi category in non tobacco users 
Real 
0.001 
rr_lower_bmi_tob 
rate ratio for lower bmi category for tobacco users 
Real 
1.4 
rr_lower_bmi_pop_advice_weight 
probability per 3 months of decrease in bmi category given population advice/campaign on weight 
Real 
1.1 
r_high_salt_urban 
probability per 3 months of high salt intake if urban 
Real 
0.003 
rr_high_salt_rural 
rate ratio for high salt if rural 
Real 
1.5 
r_not_high_salt 
probability per 3 months of not high salt intake 
Real 
0.0001 
rr_not_high_salt_pop_advice_salt 
probability per 3 months of not high salt given population advice/campaign on salt 
Real 
1.1 
r_high_sugar 
probability per 3 months of high sugar intake 
Real 
0.0001 
r_not_high_sugar 
probability per 3 months of not high sugar intake 
Real 
0.0001 
rr_not_high_sugar_pop_advice_sugar 
probability per 3 months of not high sugar given population advice/campaign on sugar 
Real 
1.1 
r_low_ex 
probability per 3 months of change from not low exercise to low exercise 
Real 
0.001 
r_not_low_ex 
probability per 3 months of change from low exercise to not low exercie 
Real 
0.0001 
rr_not_low_ex_pop_advice_exercise 
probability per 3 months of not low exercise population advice/campaign on exercise 
Real 
1.1 
rr_low_ex_f 
risk ratio for becoming low exercise if female rather than male 
Real 
0.6 
rr_low_ex_urban 
risk ratio for becoming low exercise if urban rather than rural 
Real 
2.0 
r_tob 
probability per 3 months of change from not using tobacco to using tobacco if male age 1519 wealth level 1 
Real 
0.0004 
r_not_tob 
probability per 3 months of change from tobacco using to not tobacco using 
Real 
0.0001 
rr_tob_f 
rate ratio tobacco if female 
Real 
0.1 
rr_tob_age2039 
risk ratio for tobacco using if age 2039 compared with 1519 
Real 
1.2 
rr_tob_agege40 
risk ratio for tobacco using if age >= 40 compared with 1519 
Real 
1.5 
rr_tob_wealth 
risk ratio for tobacco using per 1 higher wealth level (higher wealth level = lower wealth) 
Real 
1.3 
rr_not_tob_pop_advice_tobacco 
probability per 3 months of quitting tobacco given population advice/campaign on tobacco 
Real 
1.1 
r_ex_alc 
probability per 3 months of change from not excess alcohol to excess alcohol 
Real 
0.003 
r_not_ex_alc 
probability per 3 months of change from excess alcohol to not excess alcohol 
Real 
0.0001 
rr_ex_alc_f 
risk ratio for becoming excess alcohol if female rather than male 
Real 
0.07 
rr_not_ex_alc_pop_advice_alcohol 
probability per 3 months of not excess alcohol given population advice/campaign on alcohol 
Real 
1.1 
r_mar 
probability per 3 months of marriage when age 1530 
Real 
0.03 
r_div_wid 
probability per 3 months of becoming divorced or widowed, amongst those married 
Real 
0.01 
r_stop_ed 
probabilities per 3 months of stopping education if wealth level 5 
Real 
0.007 
rr_stop_ed_lower_wealth 
relative rate of stopping education per 1 lower wealth quantile 
Real 
1.5 
p_ed_primary 
probability at age 5 that start primary education if wealth level 5 
Real 
0.9 
rp_ed_primary_higher_wealth 
relative probability of starting school per 1 higher wealth level 
Real 
1.1 
p_ed_secondary 
probability at age 13 that start secondary education at 13 if in primary education and wealth level 5 
Real 
0.8 
rp_ed_secondary_higher_wealth 
relative probability of starting secondary school per 1 higher wealth level 
Real 
1.05 
r_improved_sanitation 
probability per 3 months of change from unimproved_sanitation true to false 
Real 
0.001 
r_clean_drinking_water 
probability per 3 months of change from drinking_water true to false 
Real 
0.001 
r_non_wood_burn_stove 
probability per 3 months of change from wood_burn_stove true to false 
Real 
0.001 
r_access_handwashing 
probability per 3 months of change from no access hand washing true to false 
Real 
0.001 
start_date_campaign_exercise_increase 
Date of campaign start for increased exercise 
Date 
20100701 00:00:00 
start_date_campaign_quit_smoking 
Date of campaign start to quit smoking 
Date 
20100701 00:00:00 
start_date_campaign_alcohol_reduction 
Date of campaign start for alcohol reduction 
Date 
20100701 00:00:00 
proportion_of_men_that_are_assumed_to_be_circumcised_at_birth 
Proportion of men that are assumed to be circumcised at birth.The men are assumed to be circumcised at birth. 
Real 
0.2128 
proportion_of_men_circumcised_at_initiation 
Proportion of men (of all ages) that are assumed to be circumcised at the initiation of thesimulation. 
Real 
0.2128 
proportion_female_sex_workers 
proportion of women aged 1549 years who are sex workers 
Real 
0.0069 
fsw_transition 
proportion of sex workers that stop being a sex worker each year 
Real 
0.18181818181818182 
init_p_urban
prop_urban
Chitipa 
Karonga 
Nkhata Bay 
Rumphi 
Mzimba 
Likoma 
Mzuzu 
Mzuzu City 
Kasungu 
Nkhotakota 
Ntchisi 
Dowa 
Salima 
Lilongwe 
Lilongwe City 
Mchinji 
Dedza 
Ntcheu 
Mangochi 
Machinga 
Zomba 
Zomba City 
Chiradzulu 
Blantyre 
Blantyre City 
Mwanza 
Thyolo 
Mulanje 
Phalombe 
Chikwawa 
Nsanje 
Balaka 
Neno 

0.1846 
0.2644 
0.1716 
0.2188 
0.0386 
0.1503 
0 
1 
0.2029 
0.1372 
0.1372 
0.1379 
0.1924 
0 
1 
0.1486 
0.1383 
0.1118 
0.1642 
0.1499 
0 
1 
0.0635 
0 
1 
0.2536 
0.1111 
0.1149 
0.0897 
0.1171 
0.2053 
0.1836 
0.1015 
Malaria
Name 
Description 
Type 
Value 

interv 
data frame of intervention coverage by year 
Dataframe 

clin_inc 
data frame of clinical incidence by age, district, intervention coverage 
Dataframe 

inf_inc 
data frame of infection incidence by age, district, intervention coverage 
Dataframe 

sev_inc 
data frame of severe case incidence by age, district, intervention coverage 
Dataframe 

itn_district 
data frame of ITN usage rates by district 
Dataframe 

irs_district 
data frame of IRS usage rates by district 
Dataframe 

sev_symp_prob 
probabilities of each symptom for severe malaria cases 
Dataframe 

sensitivity_rdt 
Sensitivity of rdt 
Real 
0.95 
cfr 
casefatality rate for severe malaria 
Real 
0.15 
dur_asym 
duration (days) of asymptomatic malaria 
Real 
110.0 
dur_clin 
duration (days) of clinical symptoms of malaria 
Real 
5.0 
dur_clin_para 
duration (days) of parasitaemia for clinical malaria cases 
Real 
195.0 
treatment_adjustment 
probability of death from severe malaria if on treatment 
Real 
0.5 
p_sev_anaemia_preg 
probability of severe anaemia in pregnant women with clinical malaria 
Real 
0.075 
mortality_adjust 
adjustment of casefatality rate to match WHO/MAP 
Real 
10.0 
data_end 
final year of ICL malaria model outputs, after 2018 = projections 
Real 
2018.0 
irs_rates_boundary 
threshold for indoor residual spraying coverage 
Real 
0.5 
irs_rates_upper 
indoor residual spraying high coverage 
Real 
0.8 
irs_rates_lower 
indoor residual spraying low coverage 
Real 
0.0 
prob_malaria_case_tests 
probability that a malaria case will have a scheduled rdt 
Real 
0.4 
itn 
projected future itn coverage 
Real 
0.6 
rdt_testing_rates 
per capita rdt testing rate of general population 
Dataframe 

scaling_factor_for_rdt_availability 
scaling factor applied to the reports of rdt usage to compensate fornonavailability of rdts at some facilities 
Real 
1.2 
duration_iptp_protection_weeks 
duration of protection against clinical malaria conferred by each dose of IPTp 
Real 
6.0 
rr_clinical_malaria_hiv_under5 
relative risk of clinical malaria if HIV+ and aged under 5 years 
Real 
1.7 
rr_clinical_malaria_hiv_over5 
relative risk of clinical malaria if HIV+ and aged over 5 years 
Real 
2.6 
rr_clinical_malaria_hiv_pregnant 
relative risk of clinical malaria if HIV+ and pregnant 
Real 
3.96 
rr_clinical_malaria_cotrimoxazole 
relative risk of clinical malaria if on cotrimoxazole 
Real 
0.58 
rr_clinical_malaria_art 
relative risk of clinical malaria if HIV+ and on ART and virally suppressed 
Real 
0.74 
rr_clinical_malaria_iptp 
relative risk of clinical malaria with each dose of IPTp 
Real 
0.54 
rr_severe_malaria_hiv_under5 
relative risk of severe malaria if HIV+ and aged under 5 years 
Real 
9.69 
rr_severe_malaria_hiv_over5 
relative risk of severe malaria if HIV+ and aged over 5 years 
Real 
2.68 
rr_severe_malaria_hiv_pregnant 
relative risk of clinical malaria if HIV+ and pregnant 
Real 
2.8 
rr_severe_malaria_iptp 
relative risk of severe malaria with each dose of IPTp 
Real 
0.6 
prob_of_treatment_success 
probability that treatment will clear malaria symptoms 
Real 
1.0 
type_of_scaleup 
argument to determine type scaleup of program which will be implemented, can be ‘none’, ‘target’ or ‘max’ 
String 
none 
scaleup_start_year 
the year when the scaleup starts (it will occur on 1st January of that year) 
Integer 
2025 
scaleup_parameters 
the parameters and values changed in scenario analysis 
Dataframe 
interv
Year 
ITN_coverage 
IRS_coverage 
ACT_coverage 
MIS_sleptUnderITN 
MIS_IPTp_1dose 
MIS_IPTp_2dose 
MIS_IPTp_3dose 

2001 
0 
0 
0 
nan 
nan 
nan 
nan 
2002 
0 
0 
0 
nan 
nan 
nan 
nan 
2003 
0.0337 
0 
0 
0.02022 
nan 
nan 
nan 
2004 
0.1149 
0 
0.011 
0.06894 
nan 
nan 
nan 
2005 
0.2636 
0 
0.0269 
0.15816 
nan 
nan 
nan 
2006 
0.2405 
0 
0.0538 
0.1443 
nan 
nan 
nan 
2007 
0.2865 
0.00712375 
0.0898 
0.1719 
nan 
nan 
nan 
2008 
0.3185 
0.00698449 
0.1382 
0.1911 
nan 
nan 
nan 
2009 
0.2908 
0.0198598 
0.2082 
0.17448 
nan 
nan 
nan 
Only first 10 rows of 26 are shown.
clin_inc
Unnamed: 0 
admin 
llin 
irs 
month 
inc_age_gp 
clin_incidence 
age 
monthly_inc_clin 
monthly_prob_clin 

1 
Balaka 
0.1 
0.8 
2 
clin_inc_0_0.5 
0.616651 
0 
0.0513875 
0.0500895 
2 
Balaka 
0.1 
0.8 
3 
clin_inc_0_0.5 
0.724266 
0 
0.0603555 
0.0585702 
3 
Balaka 
0.1 
0.8 
4 
clin_inc_0_0.5 
0.487449 
0 
0.0406208 
0.0398068 
4 
Balaka 
0.1 
0.8 
5 
clin_inc_0_0.5 
0.221309 
0 
0.0184424 
0.0182734 
5 
Balaka 
0.1 
0.8 
6 
clin_inc_0_0.5 
0.0654417 
0 
0.00545347 
0.00543863 
6 
Balaka 
0.1 
0.8 
7 
clin_inc_0_0.5 
0.00924685 
0 
0.000770571 
0.000770274 
7 
Balaka 
0.1 
0.8 
8 
clin_inc_0_0.5 
0.0258359 
0 
0.00215299 
0.00215068 
8 
Balaka 
0.1 
0.8 
9 
clin_inc_0_0.5 
0.0592395 
0 
0.00493663 
0.00492446 
9 
Balaka 
0.1 
0.8 
10 
clin_inc_0_0.5 
0.0234651 
0 
0.00195542 
0.00195351 
Only first 10 rows of 497664 are shown.
inf_inc
Unnamed: 0 
admin 
llin 
irs 
month 
inf_inc_age_gp 
inf_incidence 
age 
monthly_inc_inf 
monthly_prob_inf 

1 
Balaka 
0.1 
0.8 
2 
inf_inc_0_0.5 
1.19984 
0 
0.0999865 
0.0951504 
2 
Balaka 
0.1 
0.8 
3 
inf_inc_0_0.5 
1.42709 
0 
0.118924 
0.112125 
3 
Balaka 
0.1 
0.8 
4 
inf_inc_0_0.5 
0.955087 
0 
0.0795906 
0.0765057 
4 
Balaka 
0.1 
0.8 
5 
inf_inc_0_0.5 
0.464054 
0 
0.0386712 
0.037933 
5 
Balaka 
0.1 
0.8 
6 
inf_inc_0_0.5 
0.122824 
0 
0.0102353 
0.0101831 
6 
Balaka 
0.1 
0.8 
7 
inf_inc_0_0.5 
0.0174689 
0 
0.00145575 
0.00145469 
7 
Balaka 
0.1 
0.8 
8 
inf_inc_0_0.5 
0.0559292 
0 
0.00466077 
0.00464993 
8 
Balaka 
0.1 
0.8 
9 
inf_inc_0_0.5 
0.110247 
0 
0.00918724 
0.00914517 
9 
Balaka 
0.1 
0.8 
10 
inf_inc_0_0.5 
0.0416001 
0 
0.00346667 
0.00346067 
Only first 10 rows of 497664 are shown.
sev_inc
Unnamed: 0 
admin 
llin 
irs 
month 
sev_inc_age_gp 
sev_incidence 
age 
monthly_inc_sev 
monthly_prob_sev 

1 
Balaka 
0.1 
0.8 
2 
sev_inc_0_0.5 
0.039965 
0 
0.00333041 
0.00332487 
2 
Balaka 
0.1 
0.8 
3 
sev_inc_0_0.5 
0.0449733 
0 
0.00374778 
0.00374076 
3 
Balaka 
0.1 
0.8 
4 
sev_inc_0_0.5 
0.0293607 
0 
0.00244672 
0.00244373 
4 
Balaka 
0.1 
0.8 
5 
sev_inc_0_0.5 
0.0133483 
0 
0.00111236 
0.00111174 
5 
Balaka 
0.1 
0.8 
6 
sev_inc_0_0.5 
0.00411232 
0 
0.000342693 
0.000342634 
6 
Balaka 
0.1 
0.8 
7 
sev_inc_0_0.5 
0.000551552 
0 
4.59627e05 
4.59616e05 
7 
Balaka 
0.1 
0.8 
8 
sev_inc_0_0.5 
0.00155992 
0 
0.000129993 
0.000129985 
8 
Balaka 
0.1 
0.8 
9 
sev_inc_0_0.5 
0.00409992 
0 
0.00034166 
0.000341602 
9 
Balaka 
0.1 
0.8 
10 
sev_inc_0_0.5 
0.00162945 
0 
0.000135787 
0.000135778 
Only first 10 rows of 497664 are shown.
itn_district
District 
Year 
itn_rate 

Balaka 
2011 
0.3 
Balaka 
2012 
0.5 
Balaka 
2013 
0.7 
Balaka 
2014 
0.6 
Balaka 
2015 
0.4 
Balaka 
2016 
0.6 
Balaka 
2017 
0.6 
Balaka 
2018 
0.6 
Blantyre 
2010 
0.5 
Only first 10 rows of 288 are shown.
irs_district
District 
Year 
irs_rate 

Balaka 
2011 
0 
Balaka 
2012 
0 
Balaka 
2013 
0 
Balaka 
2014 
0 
Balaka 
2015 
0 
Balaka 
2016 
0 
Balaka 
2017 
0 
Balaka 
2018 
0 
Blantyre 
2010 
0 
Only first 10 rows of 288 are shown.
sev_symp_prob
symptom 
age_group 
prop_lower 
prop_upper 

acidosis 
0_5 
0.4 
0.45 
coma_convulsions 
0_5 
0.3 
0.4 
renal_failure 
0_5 
0.05 
0.15 
severe_anaemia 
0_5 
0.4 
0.5 
shock 
0_5 
0.05 
0.15 
jaundice 
5_60 
0.1 
0.6 
acidosis 
5_60 
0.45 
0.6 
coma_convulsions 
5_60 
0.38 
0.45 
renal_failure 
5_60 
0.1 
0.5 
Only first 10 rows of 12 are shown.
rdt_testing_rates
Year 
NumSuspectedCasesTestedByRDT 
NumPositiveCasesTestedByRDT 
NumSuspectedCasesTestedByMicroscopy 
NumPositiveCasesTestedByMicroscopy 
NumTreated 
NumMalariaCases 
TreatmentCoverage 
Population 
Rate_rdt_testing 

2011 
580708 
253973 
166959 
50526 
nan 
5.46033e+06 
nan 
1.51461e+07 
0.0383404 
2012 
2.76399e+06 
1.28185e+06 
103754 
283138 
nan 
4.92953e+06 
nan 
1.55813e+07 
0.177392 
2013 
3.02902e+06 
1.23639e+06 
129575 
44501 
nan 
4.5475e+06 
nan 
1.60248e+07 
0.189021 
2014 
5.34472e+06 
2.82768e+06 
127752 
77635 
nan 
4.26516e+06 
nan 
1.6478e+07 
0.324356 
2015 
7.03008e+06 
3.58532e+06 
240212 
75923 
nan 
4.03294e+06 
nan 
1.69389e+07 
0.415025 
2016 
8.66124e+06 
4.73084e+06 
216643 
96538 
nan 
3.86857e+06 
nan 
1.74056e+07 
0.497611 
2017 
9.41394e+06 
4.90134e+06 
198534 
46099 
nan 
3.85109e+06 
nan 
1.78812e+07 
0.526473 
2018 
1.13841e+07 
5.83074e+06 
132475 
34735 
7.04301e+06 
3.78227e+06 
1.86211 
1.83679e+07 
0.619783 
2019 
1.08613e+07 
5.15378e+06 
406907 
30328 
5.08972e+06 
3.83515e+06 
1.32712 
1.88673e+07 
0.575668 
Only first 10 rows of 15 are shown.
scaleup_parameters
parameter 
target_value 
min_value 
max_value 

prob_malaria_case_tests 
1 
0 
1 
rdt_testing_rates 
0.8 
0 
1 
prob_of_treatment_success 
1 
0 
1 
irs_district 
0.8 
0 
0.8 
itn_district 
0.7 
0 
0.7 
itn 
0.7 
0 
0.7 
Measles
Name 
Description 
Type 
Value 

beta_baseline 
Baseline measles transmission probability 
Real 
0.00216 
beta_scale 
Scale value for measles transmission probability sinusoidal function 
Real 
1.0 
phase_shift 
Phase shift for measles transmission probability sinusoidal function 
Real 
5.0 
period 
Period for measles transmission probability sinusoidal function 
Real 
12.0 
vaccine_efficacy_1 
Efficacy of first measles vaccine dose against measles infection 
Real 
0.85 
vaccine_efficacy_2 
Efficacy of second measles vaccine dose against measles infection 
Real 
0.99 
prob_severe 
Probability of severe measles infection, requiring hospitalisation 
Real 
0.05 
risk_death_on_treatment 
Risk of scheduled death occurring if on treatment for measles complications 
Real 
0.38 
symptom_prob 
Probability of each symptom with measles infection 
Dataframe 

case_fatality_rate 
Probability that case of measles will result in death if not treated 
Dictionary 
symptom_prob
age 
symptom 
probability 

1 
rash 
1 
2 
rash 
1 
3 
rash 
1 
4 
rash 
1 
5 
rash 
1 
6 
rash 
1 
7 
rash 
1 
8 
rash 
1 
9 
rash 
1 
Only first 10 rows of 217 are shown.
case_fatality_rate
0 
1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 
15 
16 
17 
18 
19 
20 
21 
22 
23 
24 
25 
26 
27 
28 
29 
30 

0.03 
0.03 
0.03 
0.03 
0.03 
0.01 
0.01 
0.01 
0.01 
0.01 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
0.00333333 
NewbornOutcomes
Name 
Description 
Type 
Value 

prob_care_seeking_for_complication 
baseline probability that a mother will seek care for an unwell neonate following delivery 
List 
[0.782, 0.782] 
prob_day_reaches_week_one_event 
Probabilities for day of attendance at postnatal week one event 
List 
[[0.4, 0.3, 0.2, 0.05, 0.05], [0.4, 0.3, 0.2, 0.05, 0.05]] 
prob_early_onset_neonatal_sepsis_day_0 
baseline probability of a neonate developing early onset sepsis between birth and 24hrs 
List 
[0.02, 0.017] 
rr_eons_maternal_chorio 
relative risk of EONS in newborns whose mothers have chorioamnionitis 
List 
[6.6, 6.6] 
rr_eons_maternal_prom 
relative risk of EONS in newborns whose mothers have PROM 
List 
[4.9, 4.9] 
rr_eons_preterm_neonate 
relative risk of EONS in preterm newborns 
List 
[3.36, 3.36] 
cfr_early_onset_sepsis 
case fatality rate for a neonate due to neonatal sepsis 
List 
[0.064, 0.056] 
cfr_late_onset_sepsis 
case fatality rate for a neonate due to neonatal sepsis 
List 
[0.064, 0.056] 
prob_mild_impairment_post_sepsis 
probability of the mild neurodevelopmental impairment in survivors of sepsis 
List 
[0.12, 0.12] 
prob_mod_severe_impairment_post_sepsis 
probability of the moderate or severe neurodevelopmental impairment in survivors of sepsis 
List 
[0.23, 0.23] 
prob_failure_to_transition 
baseline probability of a neonate developing intrapartum related complications (previously birth asphyxia) following delivery 
List 
[0.01, 0.01] 
prob_enceph_no_resus 
Probability of a newborn who was not breathing at birth, and didnt receive resuscitation, developing encephalopathy 
List 
[0.5, 0.5] 
cfr_failed_to_transition 
case fatality rate for a neonate following failure to transition 
List 
[0.2, 0.2] 
prob_encephalopathy 
baseline odds of a neonate developing encephalopathy of any severity following birth 
List 
[0.0097, 0.0097] 
rr_enceph_neonatal_sepsis 
relative risk of neonatal encephalopathy if the neonate is also septic 
List 
[8.67, 8.67] 
rr_enceph_obstructed_labour 
relative risk for encephalopathy if the mothers labour was obstructed 
List 
[3.8, 3.8] 
rr_enceph_acute_hypoxic_event 
relative risk for encephalopathy if the mothers experience an acute event in labour 
List 
[8.74, 8.74] 
prob_enceph_severity 
probability of the severity of encephalopathy in a newborn who is encephalopathic 
List 
[[0.422, 0.338, 0.24], [0.422, 0.338, 0.24]] 
prob_mild_impairment_post_enceph 
probability of the mild neurodevelopmental impairment in survivors of encephalopathy 
List 
[0.21, 0.21] 
prob_mod_severe_impairment_post_enceph 
probability of the moderate or severe neurodevelopmental impairment in survivors of encephalopathy 
List 
[0.269, 0.269] 
cfr_enceph 
case fatality rate for a neonate due to mild encephalopathy 
List 
[0.48, 0.28] 
cfr_multiplier_severe_enceph 
multiplier for risk of death in a neonate with severe encephalopathy 
List 
[1.91, 3.28] 
prob_respiratory_distress_preterm 
probability that a preterm infant will experience respiratory distress at birth 
List 
[0.12, 0.12] 
rr_rds_early_preterm 
relative risk of RDS in a preterm newborn born before 34 weeks 
List 
[2.64, 2.64] 
rr_rds_maternal_diabetes_mellitus 
relative risk of RDS in a preterm newborn whose mother has DM 
List 
[2.66, 2.66] 
rr_rds_maternal_gestational_diab 
relative risk of RDS in a preterm newborn whose mother has gestational diabetes 
List 
[1.57, 1.57] 
cfr_respiratory_distress_syndrome 
case fatality rate for respiratory distress syndrome of prematurity 
List 
[0.29, 0.2] 
prob_mild_disability_preterm_<32weeks 
probability of mild long term neurodevelopmental disability in preterm infants born at less than 32 weeks gestation 
List 
[0.324, 0.324] 
prob_mod_severe_disability_preterm_<32weeks 
probability of moderate/severe longterm neurodevelopmental disability in preterm infants born at less than 32 weeks gestation 
List 
[0.246, 0.246] 
prob_mild_disability_preterm_32_36weeks 
probability of mild long term neurodevelopmental disability in preterm infants born between 32 and 36 weeks gestation 
List 
[0.034, 0.034] 
prob_mod_severe_disability_preterm_32_36weeks 
probability of moderate/severe long term neurodevelopmental disability in preterm infants born between 32 and 36 weeks gestation 
List 
[0.018, 0.018] 
prob_retinopathy_preterm_early 
Probability that a neonate born at less than 32 weeks who survives the neonatal period will develop retinopathy 
List 
[0.365, 0.365] 
prob_retinopathy_preterm_late 
Probability that a neonate born at less than 32 weeks who survives the neonatal period will develop retinopathy 
List 
[0.077, 0.077] 
prob_retinopathy_severity_no_treatment 
Probabilities that a preterm neonate who developed retinopathy will experience the following vision impairments: none, mild, moderate or blindness 
List 
[[0.28, 0.03, 0.1, 0.12, 0.47], [0.28, 0.03, 0.1, 0.12, 0.47]] 
cfr_preterm_birth 
case fatality rate for a neonate born prematurely 
List 
[0.0227, 0.0187] 
rr_preterm_death_early_preterm 
relative risk of preterm death in early preterm neonates 
List 
[1.66, 1.66] 
prob_preterm_death_by_day 
probability of death due to preterm complications occurring on days 014 
List 
[[0.4, 0.2, 0.15, 0.05, 0.02, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018], [0.4, 0.2, 0.15, 0.05, 0.02, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018]] 
prob_congenital_heart_anomaly 
Probability of a congenital heart anomaly in the newborn 
List 
[0.009, 0.009] 
prob_limb_musc_skeletal_anomaly 
Probability of a congenital limb or musculoskeletal anomaly in the newborn 
List 
[0.008, 0.008] 
prob_urogenital_anomaly 
Probability of a congenital urogenital anomaly in the newborn 
List 
[0.003, 0.003] 
prob_digestive_anomaly 
Probability of a congenital digestive anomaly in the newborn 
List 
[0.0007, 0.0007] 
prob_other_anomaly 
Probability of a other congenital anomalies in the newborn 
List 
[0.0004, 0.0004] 
cfr_congenital_heart_anomaly 
case fatality rate for newborns with congenital heart anomalies 
List 
[0.062, 0.062] 
cfr_limb_or_musculoskeletal_anomaly 
case fatality rate for newborns with congenital limb/musculoskeletal anomalies 
List 
[0.0069, 0.0069] 
cfr_urogenital_anomaly 
case fatality rate for newborns with congenital urogenital anomalies 
List 
[0.0085, 0.0085] 
cfr_digestive_anomaly 
case fatality rate for newborns with congenital digestive anomalies 
List 
[0.2829, 0.2829] 
cfr_other_anomaly 
case fatality rate for newborns with other congenital anomalies 
List 
[0.131, 0.131] 
prob_cba_death_by_age_group 
probabilities that death from a congenital birth anomaly will occur once the individual reaches the following age groups: early neonatal, late neonatal, post neonatal 14 years, 59 years, 10 14 years or 1569 years 
List 
[[0.27, 0.08, 0.38, 0.2, 0.02, 0.01, 0.04], [0.3, 0.09, 0.35, 0.18, 0.03, 0.02, 0.03]] 
prob_early_breastfeeding_hb 
probability that a neonate will be breastfed within the first hour following birth when delivered at home 
List 
[0.94, 0.67] 
prob_breastfeeding_type 
probabilities that a woman is 1.) not breastfeeding 2.) nonexclusively breastfeeding 3.)exclusively breastfeeding at birth (until 6 months) 
List 
[[0.005, 0.277, 0.718], [0.101, 0.289, 0.61]] 
prob_early_breastfeeding_hf 
probability that a neonate will be breastfed within the first hour following birth when delivered at a health facility 
List 
[0.94, 0.77] 
prob_pnc_check_newborn 
probability that a neonate will receive a full postnatal check 
List 
[0.6, 0.6] 
prob_timings_pnc_newborns 
probabilities that a postnatal check will happen before or after 48 hours alive 
List 
[[0.97, 0.03], [0.97, 0.03]] 
prob_kmc_available 
probability that KMC can be delivered in a given hospital 
List 
[0.62, 0.62] 
treatment_effect_inj_abx_sep 
effect of injectable antibiotics treatment on reducing mortality from sepsis 
List 
[0.35, 0.35] 
treatment_effect_supp_care_sep 
effect of full supportive care treatment on reducing mortality from sepsis 
List 
[0.2, 0.2] 
treatment_effect_cord_care 
effect of full supportive care treatment on reducing incidence of sepsis 
List 
[0.77, 0.77] 
treatment_effect_clean_birth 
effect of clean birth practices on reducing incidence of sepsis 
List 
[0.73, 0.73] 
treatment_effect_early_init_bf 
effect of early initiation of breastfeeding on reducing incidence of sepsis 
List 
[0.55, 0.55] 
treatment_effect_resuscitation 
effect of resuscitation on newborn mortality associated with encephalopathy 
List 
[0.63, 0.63] 
treatment_effect_resuscitation_preterm 
effect of resuscitation on newborn mortality associated with prematurity 
List 
[0.81, 0.81] 
treatment_effect_abx_prom 
effect of antibiotics given to mothers experience PROM on risk of newborn sepsis 
List 
[0.67, 0.67] 
treatment_effect_steroid_preterm 
relative risk of death for preterm neonates following administration of antenatal corticosteroids 
List 
[0.71, 0.71] 
treatment_effect_kmc 
treatment effect of kangaroo mother care on preterm mortality 
List 
[0.49, 0.49] 
OesophagealCancer
Name 
Description 
Type 
Value 

init_prop_oes_cancer_stage 
initial proportions in dysplasia/cancer categories for man aged 20 with no excess alcohol and no tobacco 
List 
[0.0003, 0.0001, 5e06, 3e05, 5e05, 1e05] 
init_prop_dysphagia_oes_cancer_by_stage 
initial proportions of those with dysplasia/cancer categories that have the symptom dysphagia 
List 
[0.01, 0.03, 0.1, 0.2, 0.3, 0.8] 
init_prop_with_dysphagia_diagnosed_oes_cancer_by_stage 
initial proportions of people that have symptom of dysphagia that have been diagnosed 
List 
[0.8, 0.85, 0.9, 0.95, 0.98, 0.9] 
init_prop_treatment_status_oes_cancer 
initial proportions of people with oesophageal dysplasia/cancer that had initiated treatment 
List 
[0.01, 0.01, 0.05, 0.05, 0.05, 0.05] 
init_prob_palliative_care 
initial probability of being under palliative care if in stage 4 
Real 
0.5 
r_low_grade_dysplasia_none 
probabilty per 3 months of incident low grade oesophageal dysplasia, amongst people with no oesophageal dysplasia (men, age20, no excess alcohol, no tobacco) 
Real 
5e07 
rr_low_grade_dysplasia_none_female 
rate ratio for low grade oesophageal dysplasia for females 
Real 
1.3 
rr_low_grade_dysplasia_none_per_year_older 
rate ratio for low grade oesophageal dysplasia per year older from age 20 
Real 
1.1 
rr_low_grade_dysplasia_none_tobacco 
rate ratio for low grade oesophageal dysplasia for tobacco smokers 
Real 
2.0 
rr_low_grade_dysplasia_none_ex_alc 
rate ratio for low grade oesophageal dysplasia for no excess alcohol 
Real 
1.0 
r_high_grade_dysplasia_low_grade_dysp 
probabilty per 3 months of high grade oesophageal dysplasia, amongst people with low grade dysplasia 
Real 
0.03 
rr_high_grade_dysp_undergone_curative_treatment 
rate ratio for high grade dysplasia for people with low grade dysplasia if had curative treatment at low grade dysplasia stage 
Real 
0.1 
r_stage1_high_grade_dysp 
probabilty per 3 months of stage 1 oesophageal cancer amongst people with high grade dysplasia 
Real 
0.01 
rr_stage1_undergone_curative_treatment 
rate ratio for stage 1 oesophageal cancer for people with high grade dysplasia if had curative treatment at high grade dysplasia stage 
Real 
0.1 
r_stage2_stage1 
probabilty per 3 months of stage 2 oesophageal cancer amongst people with stage 1 
Real 
0.05 
rr_stage2_undergone_curative_treatment 
rate ratio for stage 2 oesophageal cancer for people with stage 1 oesophageal cancer if had curative treatment at stage 1 
Real 
0.1 
r_stage3_stage2 
probabilty per 3 months of stage 3 oesophageal cancer amongst people with stage 2 
Real 
0.05 
rr_stage3_undergone_curative_treatment 
rate ratio for stage 3 oesophageal cancer for people with stage 2 oesophageal cancer if had curative treatment at stage 2 
Real 
0.1 
r_stage4_stage3 
probabilty per 3 months of stage 4 oesophageal cancer amongst people with stage 3 
Real 
0.05 
rr_stage4_undergone_curative_treatment 
rate ratio for stage 4 oesophageal cancer for people with stage 3 oesophageal cancer if had curative treatment at stage 3 
Real 
0.3 
rate_palliative_care_stage4 
prob palliative care this 3 month period if stage4 
Real 
0.5 
r_death_oesoph_cancer 
probabilty per 3 months of death from oesophageal cancer mongst people with stage 4 oesophageal cancer 
Real 
0.4 
rr_dysphagia_low_grade_dysp 
probability per 3 months of dysphagia in a person with low grade oesophageal dysplasia 
Real 
1.0 
rr_dysphagia_high_grade_dysp 
rate ratio for dysphagia if have high grade oesophageal dysplasia 
Real 
1.0 
r_dysphagia_stage1 
rate ratio for dysphagia if have stage 1 oesophageal cancer 
Real 
0.01 
rr_dysphagia_stage2 
rate ratio for dysphagia if have stage 2 oesophageal cancer 
Real 
2.0 
rr_dysphagia_stage3 
rate ratio for dysphagia if have stage 3 oesophageal cancer 
Real 
50.0 
rr_dysphagia_stage4 
rate ratio for dysphagia if have stage 4 oesophageal cancer 
Real 
100.0 
rp_oes_cancer_female 
relative prevalence at baseline of oesophageal dysplasia/cancer if female 
Real 
1.3 
rp_oes_cancer_per_year_older 
relative prevalence at baseline of oesophageal dysplasia/cancer per year older than 20 
Real 
1.1 
rp_oes_cancer_tobacco 
relative prevalence at baseline of oesophageal dysplasia/cancer if tobacco 
Real 
2.0 
rp_oes_cancer_ex_alc 
relative prevalence at baseline of oesophageal dysplasia/cancer 
Real 
1.0 
sensitivity_of_endoscopy_for_oes_cancer_with_dysphagia 
sensitivity of endoscopy_for diagnosis of oesophageal cancer for those with dysphagia 
Real 
1.0 
OtherAdultCancer
Name 
Description 
Type 
Value 

init_prop_early_other_adult_ca_symptom_other_adult_cancer_by_stage 
initial proportions of those with other adult cancer categories that have other adult_ca_symptom 
List 
[0.3, 0.5, 0.8] 
in_prop_other_adult_cancer_stage 
initial proportions in other adult cancer stages for person aged 1529 
List 
[0.0002, 0.0002, 0.0004] 
init_prop_with_early_other_adult_ca_symptom_diagnosed_by_stage 
initial proportions of people that have symptom of other_adult_ca_symptom that have been diagnosed 
List 
[0.3, 0.4, 0.5] 
init_prop_treatment_status_other_adult_cancer 
initial proportions of people with other_adult cancer previously given treatment 
List 
[0.1, 0.1, 0.1] 
init_prob_palliative_care 
initial probability of being under palliative care if in metastatic 
Real 
0.95 
r_site_confined_none 
probabilty per 3 months of incident site_confined other_adult cancer amongst people age 1529 with no other adult cancer 
Real 
1e05 
rr_site_confined_age3049 
rate ratio for siteconfined other_adult cancer for age 3049 
Real 
5.0 
rr_site_confined_age5069 
rate ratio for siteconfined other_adult cancer for age 5069 
Real 
21.0 
rr_site_confined_agege70 
rate ratio for siteconfined other_adult cancer for age ge 70 
Real 
60.0 
rr_site_confined_hiv 
rate ratio for siteconfined other_adult_cancer if infected with HIV 
Real 
4.13 
r_local_ln_site_confined_other_adult_ca 
probabilty per 3 months of local ln other_adult cancer amongst people with site confined 
Real 
0.15 
rr_local_ln_other_adult_ca_undergone_curative_treatment 
rate ratio for local_ln for people with site_confined if had curative treatment at site_confined stage 
Real 
0.1 
r_metastatic_local_ln 
probabilty per 3 months of metastatic other_adult cancer amongst people with local_ln 
Real 
0.15 
rr_metastatic_undergone_curative_treatment 
rate ratio for metastatic Other_adult cancer for people with local_lnOther_adult cancer if had curative treatment at local_ln 
Real 
0.2 
r_death_other_adult_cancer 
probabilty per 3 months of death from other adult cancer mongst people with metastatic other_adult cancer 
Real 
0.2 
r_early_other_adult_ca_symptom_site_confined_other_adult_ca 
probability per 3 months of other_adult_ca_symptom in a person with site confined other_adult cancer 
Real 
0.02 
rr_early_other_adult_ca_symptom_local_ln_other_adult_ca 
rate ratio for other_adult_ca_symptom if have high grade other_adult cancer 
Real 
3.0 
rr_early_other_adult_ca_symptom_metastatic_other_adult_ca 
rate ratio for other_adult_ca_symptom if have metastatic other_adult cancer 
Real 
10.0 
rp_other_adult_cancer_age3049 
relative prevalence at baseline of bladder cancer/cancer age 3049 
Real 
1.5 
rp_other_adult_cancer_age5069 
relative prevalence at baseline of bladder cancer/cancer age 5069 
Real 
2.0 
rp_other_adult_cancer_agege70 
relative prevalence at baseline of bladder cancer/cancer age 70+ 
Real 
4.0 
sensitivity_of_diagnostic_device_for_other_adult_cancer_with_other_adult_ca_site_confined 
sensitivity of diagnostic_device_for diagnosis of other_adult cancer for those with other_adult_ca_siteconfined 
Real 
0.8 
sensitivity_of_diagnostic_device_for_other_adult_cancer_with_other_adult_ca_local_ln 
sensitivity of diagnostic_device_for diagnosis of other_adult cancer for those with other_adult_local_ln 
Real 
0.95 
sensitivity_of_diagnostic_device_for_other_adult_cancer_with_other_adult_ca_metastatic 
sensitivity of diagnostic_device_for diagnosis of other_adult cancer for those with other_adult_ca metastatic 
Real 
0.95 
PostnatalSupervisor
Name 
Description 
Type 
Value 

prob_obstetric_fistula 
probability of a woman developing an obstetric fistula after birth 
List 
[0.00426, 0.00426] 
rr_obstetric_fistula_obstructed_labour 
relative risk of obstetric fistula in women who experienced obstructed labour 
List 
[14.8, 14.8] 
prevalence_type_of_fistula 
prevalence of 1.) vesicovaginal 2.)rectovaginal fistula 
List 
[[0.924, 0.076], [0.924, 0.076]] 
prob_secondary_pph 
baseline probability of secondary PPH 
List 
[0.0002, 0.00034] 
rr_secondary_pph_endometritis 
relative risk of secondary postpartum haemorrhage in women with sepsis secondary to endometritis 
List 
[1, 1] 
prob_secondary_pph_severity 
probability of mild, moderate or severe secondary PPH 
List 
[[0.33, 0.33, 0.34], [0.33, 0.33, 0.34]] 
cfr_secondary_postpartum_haemorrhage 
case fatality rate for secondary pph 
List 
[0.22, 0.08] 
prob_htn_resolves 
Weekly probability of resolution of hypertension 
List 
[0.167, 0.167] 
weekly_prob_gest_htn_pn 
weekly probability of a woman developing gestational hypertension during the postnatal period 
List 
[0.0025, 0.0025] 
rr_gest_htn_obesity 
Relative risk of gestational hypertension for women who are obese 
List 
[3.31, 3.31] 
weekly_prob_pre_eclampsia_pn 
weekly probability of a woman developing mild preeclampsia during the postnatal period 
List 
[0.0017, 0.0017] 
rr_pre_eclampsia_obesity 
Relative risk of preeclampsia for women who are obese 
List 
[3.2, 3.2] 
rr_pre_eclampsia_chronic_htn 
Relative risk of preeclampsia in women who are chronically hypertensive 
List 
[2.26, 2.26] 
rr_pre_eclampsia_diabetes_mellitus 
Relative risk of preeclampsia in women who have diabetes mellitus 
List 
[3.7, 3.7] 
probs_for_mgh_matrix_pn 
probability of mild gestational hypertension moving between states: gestational hypertension, severe gestational hypertension, mild preeclampsia, severe preeclampsia, eclampsia 
List 
[[0.918, 0.032, 0.05, 0, 0], [0.918, 0.032, 0.05, 0, 0]] 
probs_for_sgh_matrix_pn 
probability of severe gestational hypertension moving between states: gestational hypertension, severe gestational hypertension, mild preeclampsia, severe preeclampsia, eclampsia 
List 
[[0, 0.92, 0, 0.08, 0], [0, 0.92, 0, 0.08, 0]] 
probs_for_mpe_matrix_pn 
probability of mild preeclampsia moving between states: gestational hypertension, severe gestational hypertension, mild preeclampsia, severe preeclampsia, eclampsia 
List 
[[0, 0, 0.95, 0.05, 0], [0, 0, 0.95, 0.05, 0]] 
probs_for_spe_matrix_pn 
probability of severe preeclampsia moving between states: gestational hypertension, severe gestational hypertension, mild preeclampsia, severe preeclampsia, eclampsia 
List 
[[0, 0, 0, 0.95, 0.05], [0, 0, 0, 0.95, 0.05]] 
probs_for_ec_matrix_pn 
probability of eclampsia moving between states: gestational hypertension, severe gestational hypertension, mild preeclampsia, severe preeclampsia, eclampsia 
List 
[[0, 0, 0, 0, 1], [0, 0, 0, 0, 1]] 
cfr_eclampsia 
case fatality rate of eclampsia in the postnatal period 
List 
[0.028, 0.03] 
cfr_severe_pre_eclampsia 
case fatality rate of severe preeclampsia in the postnatal period 
List 
[0.018, 0.018] 
weekly_prob_death_severe_gest_htn 
weekly risk of death from severe hypertension in the postnatal period 
List 
[2e05, 2e05] 
baseline_prob_anaemia_per_week 
Weekly probability of anaemia in pregnancy 
List 
[0.017, 0.024] 
rr_anaemia_maternal_malaria 
relative risk of anaemia secondary to malaria infection 
List 
[1.45, 1.45] 
rr_anaemia_recent_haemorrhage 
relative risk of anaemia secondary to recent haemorrhage 
List 
[1.93, 1.93] 
rr_anaemia_hiv_no_art 
relative risk of anaemia for a woman with HIV not on ART 
List 
[4.19, 4.19] 
prob_type_of_anaemia_pn 
probability of a woman with anaemia having mild, moderate or severe anaemia 
List 
[[0.52, 0.475, 0.005], [0.52, 0.475, 0.005]] 
prob_late_sepsis_endometritis 
probability of developing sepsis following postpartum endometritis infection 
List 
[6.9e05, 6.2e05] 
rr_sepsis_endometritis_post_cs 
relative risk of endometritis following caesarean delivery 
List 
[12.1, 12.1] 
prob_late_sepsis_urinary_tract 
probability of developing sepsis following postpartum UTI 
List 
[5.4e05, 5.4e05] 
prob_late_sepsis_skin_soft_tissue 
probability of developing sepsis following postpartum skin/soft tissue infection 
List 
[3.9e05, 3.5e05] 
rr_sepsis_sst_post_cs 
relative risk of skin/soft tissue sepsis following caesarean delivery 
List 
[3.9, 3.9] 
cfr_postpartum_sepsis 
case fatality rate for postnatal sepsis 
List 
[0.75, 0.49] 
prob_early_onset_neonatal_sepsis_week_1 
Baseline probability of a newborn developing sepsis in week one of life 
List 
[0.02, 0.017] 
rr_eons_maternal_chorio 
relative risk of EONS in newborns whose mothers have chorioamnionitis 
List 
[6.6, 6.6] 
rr_eons_maternal_prom 
relative risk of EONS in newborns whose mothers have PROM 
List 
[4.9, 4.9] 
rr_eons_preterm_neonate 
relative risk of EONS in preterm newborns 
List 
[3.36, 3.36] 
cfr_early_onset_neonatal_sepsis 
case fatality for early onset neonatal sepsis 
List 
[0.064, 0.056] 
prob_late_onset_neonatal_sepsis 
probability of late onset neonatal sepsis (all cause) 
List 
[0.0045, 0.0038] 
cfr_late_neonatal_sepsis 
Risk of death from late neonatal sepsis 
List 
[0.064, 0.056] 
prob_sepsis_disabilities 
Probabilities of varying disability levels after neonatal sepsis 
List 
[[0.4, 0.1, 0.3, 0.1, 0.1], [0.4, 0.1, 0.3, 0.1, 0.1]] 
prob_care_seeking_postnatal_emergency 
baseline probability of emergency care seeking for women in the postnatal period 
List 
[0.782, 0.782] 
prob_care_seeking_postnatal_emergency_neonate 
baseline probability care will be sought for a neonate with a complication 
List 
[0.782, 0.782] 
odds_care_seeking_fistula_repair 
odds of a woman seeking care for treatment of obstetric fistula 
List 
[1.5, 1.5] 
aor_cs_fistula_age_15_19 
odds ratio for care seeking for treatment of obstetric fistula in 1519 year olds 
List 
[0.31, 0.31] 
aor_cs_fistula_age_lowest_education 
odds ratio for care seeking for treatment of obstetric fistula in women in the lowest education quantile 
List 
[0.69, 0.69] 
treatment_effect_early_init_bf 
effect of early initiation of breastfeeding on neonatal sepsis rates 
List 
[0.55, 0.55] 
treatment_effect_iron_folic_acid_anaemia 
effect of iron and folic acid supplementation on anaemia risk 
List 
[0.3, 0.3] 
treatment_effect_abx_prom 
effect of early antibiotics given to a mother with PROM on neonatal sepsis rates 
List 
[0.67, 0.67] 
treatment_effect_clean_birth 
Treatment effect of clean birth practices on early onset neonatal sepsis risk 
List 
[0.73, 0.73] 
treatment_effect_cord_care 
Treatment effect of chlorhexidine cord care on early onset neonatal sepsis risk 
List 
[0.77, 0.77] 
treatment_effect_anti_htns_progression_pn 
Treatment effect of oral anti hypertensives on progression from mild/mod to severe gestationalhypertension 
List 
[0.49, 0.49] 
PregnancySupervisor
Name 
Description 
Type 
Value 

prob_ectopic_pregnancy 
probability of ectopic pregnancy 
List 
[0.01, 0.01] 
prob_care_seeking_ectopic_pre_rupture 
probability a woman will seek care for ectopic pregnancy prior to rupture 
List 
[0.08, 0.08] 
prob_ectopic_pregnancy_death 
probability of a woman dying from a ruptured ectopic pregnancy 
List 
[0.02, 0.012] 
prob_multiples 
probability that a woman is currently carrying more than one pregnancy 
List 
[0.0399, 0.0399] 
prob_placenta_praevia 
probability that this womans pregnancy will be complicated by placenta praevia 
List 
[0.005, 0.0058] 
rr_placenta_praevia_previous_cs 
relative risk of placenta praevia in a woman who has previously delivered via caesarean section 
List 
[1.47, 1.47] 
prob_syphilis_during_pregnancy 
probability that this womans will develop syphilis during her pregnancy 
List 
[0.028, 0.028] 
prob_previous_miscarriage_at_baseline 
probability that a woman at baseline will have previously experienced a miscarriage 
Real 
0.047 
prob_spontaneous_abortion_per_month 
underlying risk of spontaneous abortion per month 
List 
[[0.025, 0.037, 0.05, 0.037, 0.025], [0.025, 0.037, 0.05, 0.037, 0.025]] 
rr_spont_abortion_age_35 
relative risk of spontaneous abortion in women aged 35 years or older 
List 
[4, 4] 
rr_spont_abortion_age_31_34 
relative risk of spontaneous abortion in women aged 3134 years old 
List 
[2.31, 2.31] 
rr_spont_abortion_prev_sa 
relative risk of spontaneous abortion in women who have previously experiences spontaneous abortion 
List 
[2.23, 2.23] 
prob_complicated_sa 
probability that a woman who experiences spontaneous abortion with experience any complications 
List 
[0.11, 0.11] 
prob_induced_abortion_per_month 
underlying risk of induced abortion per month 
List 
[0.038, 0.038] 
prob_complicated_ia 
probability that a woman who experiences induced abortion with experience any complications 
List 
[0.37, 0.37] 
prob_haemorrhage_post_abortion 
probability of haemorrhage following an abortion 
List 
[0.23, 0.23] 
prob_sepsis_post_abortion 
probability of sepsis following an abortion 
List 
[0.137, 0.137] 
prob_injury_post_abortion 
probability of injury following an abortion 
List 
[0.056, 0.056] 
prob_induced_abortion_death 
underlying risk of death following an induced abortion 
List 
[0.005, 0.0025] 
prob_spontaneous_abortion_death 
underlying risk of death following an spontaneous abortion 
List 
[0.01, 0.005] 
baseline_prob_anaemia_per_month 
baseline risk of a woman developing anaemia secondary only to pregnant 
List 
[0.1, 0.12] 
rr_anaemia_maternal_malaria 
relative risk of anaemia secondary to malaria infection 
List 
[1.45, 1.45] 
rr_anaemia_hiv_no_art 
relative risk of anaemia for a woman with HIV not on ART 
List 
[4.19, 4.19] 
prob_mild_mod_sev_anaemia 
probabilities that a womans anaemia will be mild, moderate or severe 
List 
[[0.52, 0.475, 0.005], [0.5, 0.46, 0.04]] 
prob_gest_diab_per_month 
underlying risk of gestational diabetes per month without the impact of risk factors 
List 
[0.0056, 0.0056] 
rr_gest_diab_obesity 
Relative risk of gestational diabetes for women who are obese 
List 
[3.97, 3.97] 
prob_gest_htn_per_month 
underlying risk of gestational hypertension per month without the impact of risk factors 
List 
[0.0073, 0.0073] 
rr_gest_htn_obesity 
Relative risk of gestational hypertension for women who are obese 
List 
[3.31, 3.31] 
prob_pre_eclampsia_per_month 
underlying risk of preeclampsia per month without the impact of risk factors 
List 
[0.0065, 0.0065] 
rr_pre_eclampsia_obesity 
Relative risk of preeclampsia for women who are obese 
List 
[3.2, 3.2] 
rr_pre_eclampsia_multiple_pregnancy 
Relative risk of preeclampsia for women who are pregnant with twins 
List 
[4.07, 4.07] 
rr_pre_eclampsia_chronic_htn 
Relative risk of preeclampsia in women who are chronically hypertensive 
List 
[2.26, 2.26] 
rr_pre_eclampsia_diabetes_mellitus 
Relative risk of preeclampsia in women who have diabetes mellitus 
List 
[3.7, 3.7] 
probs_for_mgh_matrix 
probability of mild gestational hypertension moving between states: gestational hypertension, severe gestational hypertension, mild preeclampsia, severe preeclampsia, eclampsia 
List 
[[0.918, 0.032, 0.05, 0, 0], [0.918, 0.032, 0.05, 0, 0]] 
probs_for_sgh_matrix 
probability of severe gestational hypertension moving between states: gestational hypertension, severe gestational hypertension, mild preeclampsia, severe preeclampsia, eclampsia 
List 
[[0, 0.87, 0, 0.13, 0], [0, 0.87, 0, 0.13, 0]] 
probs_for_mpe_matrix 
probability of mild preeclampsia moving between states: gestational hypertension, severe gestational hypertension, mild preeclampsia, severe preeclampsia, eclampsia 
List 
[[0, 0, 0.78, 0.22, 0], [0, 0, 0.78, 0.22, 0]] 
probs_for_spe_matrix 
probability of severe preeclampsia moving between states: gestational hypertension, severe gestational hypertension, mild preeclampsia, severe preeclampsia, eclampsia 
List 
[[0, 0, 0, 0.16, 0.84], [0, 0, 0, 0.16, 0.84]] 
probs_for_ec_matrix 
probability of eclampsia moving between states: gestational hypertension, severe gestational hypertension, mild preeclampsia, severe preeclampsia, eclampsia 
List 
[[0, 0, 0, 0, 1], [0, 0, 0, 0, 1]] 
prob_severe_pre_eclampsia_death 
probability of death for a woman experiencing acute severe preeclampsia 
List 
[0.018, 0.018] 
prob_eclampsia_death 
probability of death for a woman experiencing eclampsia 
List 
[0.028, 0.03] 
prob_monthly_death_severe_htn 
monthly risk of death for a woman with severe hypertension 
List 
[0.0001, 0.0001] 
prob_placental_abruption_per_month 
monthly probability that a woman will develop placental abruption 
List 
[0.0005, 0.0005] 
rr_placental_abruption_hypertension 
Relative risk of placental abruption in women with hypertension 
List 
[2.2, 2.2] 
rr_placental_abruption_previous_cs 
Relative risk of placental abruption in women who delivered previously via caesarean section 
List 
[1.3, 1.3] 
prob_aph_placenta_praevia 
risk of antepartum haemorrhage due to ongoing placenta praevia 
List 
[0.09, 0.09] 
prob_aph_placental_abruption 
risk of antepartum haemorrhage due to placental abruption 
List 
[0.9, 0.9] 
prob_mod_sev_aph 
probabilities that APH is mild/moderate or severe 
List 
[[0.8, 0.2], [0.8, 0.2]] 
prob_antepartum_haemorrhage_death 
probability of death for a woman suffering acute antepartum haemorrhage 
List 
[0.11, 0.04] 
prob_prom_per_month 
monthly probability that a woman will experience premature rupture of membranes 
List 
[0.0064, 0.0064] 
prob_chorioamnionitis 
monthly probability of a women developing chorioamnionitis 
List 
[0.015, 0.013] 
prob_antenatal_sepsis_death 
case fatality rate for chorioamnionitis 
List 
[0.75, 0.49] 
baseline_prob_early_labour_onset 
monthly baseline risk of labour onsetting before term 
List 
[[0.0008, 0.0033, 0.017, 0.04], [0.0008, 0.0033, 0.017, 0.04]] 
rr_preterm_labour_post_prom 
relative risk of early labour onset following PROM 
List 
[5.9, 5.9] 
rr_preterm_labour_anaemia 
relative risk of early labour onset in women with anaemia 
List 
[4.58, 4.58] 
rr_preterm_labour_malaria 
relative risk of early labour onset in women with malaria 
List 
[3.08, 3.08] 
rr_preterm_labour_multiple_pregnancy 
relative risk of early labour onset in women pregnant with twins 
List 
[3.44, 3.44] 
prob_still_birth_per_month 
underlying risk of stillbirth per month without the impact of risk factors 
List 
[0.0031, 0.0026] 
rr_still_birth_ga_41 
relative risk of still birth in women with gestational age 41 weeks 
List 
[2.24, 2.24] 
rr_still_birth_ga_42 
relative risk of still birth in women with gestational age 42 weeks 
List 
[3.88, 3.88] 
rr_still_birth_ga_>42 
relative risk of still birth in women with gestational age > 42 weeks 
List 
[6.94, 6.94] 
rr_still_birth_gest_diab 
relative risk of still birth in women with gestational diabetes 
List 
[3.91, 3.91] 
rr_still_birth_diab_mellitus 
relative risk of still birth in women with diabetes mellitus 
List 
[3.52, 3.52] 
rr_still_birth_maternal_malaria 
relative risk of still birth in women with malaria 
List 
[1.81, 1.81] 
rr_still_birth_maternal_syphilis 
relative risk of still birth in women with syphilis 
List 
[6.87, 6.87] 
rr_still_birth_pre_eclampsia 
relative risk of still birth in women with preeclampsia 
List 
[4.15, 4.15] 
rr_still_birth_eclampsia 
relative risk of still birth in women with eclampsia 
List 
[4.15, 4.15] 
rr_still_birth_gest_htn 
relative risk of still birth in women with mild gestational hypertension 
List 
[1.21, 1.21] 
rr_still_birth_chronic_htn 
relative risk of still birth in women with chronic hypertension 
List 
[2.32, 2.23] 
rr_still_birth_aph 
relative risk of still birth in women with antepartum haemorrhage 
List 
[2.1, 2.1] 
rr_still_birth_chorio 
relative risk of still birth in women with chorioamnionitis 
List 
[2, 2] 
prob_seek_care_pregnancy_complication 
Probability that a woman who is pregnant will seek care in the event of a complication 
List 
[0.782, 0.782] 
prob_seek_care_pregnancy_loss 
Probability that a woman who has developed complications post pregnancy loss will seek care 
List 
[0.782, 0.782] 
prob_seek_care_induction 
Probability that a woman who is post term will seek care for induction of labour 
List 
[0.2, 0.2] 
prob_anc1_months_2_to_4 
list of probabilities that a woman will attend her first ANC visit at either month 2, 3 or 4 of pregnancy 
List 
[[0.165, 0.165, 0.67], [0.165, 0.364, 0.471]] 
prob_anc1_months_5_to_9 
list of probabilities that a woman will attend her first ANC visit on months 510 
List 
[[0.345, 0.245, 0.28, 0.015, 0.015, 0.1], [0.41, 0.25, 0.21, 0.015, 0.015, 0.1]] 
odds_early_init_anc4 
probability of a woman undergoing 4 or more basic ANC visits with the first visit occurring prior or during month 4 of pregnancy (EANC4+) 
List 
[0.32, 0.58] 
aor_early_anc4_20_24 
adjusted odds ratio of EANC4+ in women aged 2024 
List 
[1.26, 1.26] 
aor_early_anc4_25_29 
adjusted odds ratio of EANC4+ in women aged 2529 
List 
[1.44, 1.44] 
aor_early_anc4_30_34 
adjusted odds ratio of EANC4+ in women aged 3034 
List 
[1.49, 1.49] 
aor_early_anc4_35_39 
adjusted odds ratio of EANC4+ in women aged 3539 
List 
[1.64, 1.64] 
aor_early_anc4_40_44 
adjusted odds ratio of EANC4+ in women aged 4044 
List 
[1.51, 1.51] 
aor_early_anc4_45_49 
adjusted odds ratio of EANC4+ in women aged 4549 
List 
[1.91, 1.91] 
aor_early_anc4_2010 
adjusted odds ratio of EANC4+ in 2010 
List 
[1.51, 1.51] 
aor_early_anc4_2015 
adjusted odds ratio of EANC4+ in 2015 
List 
[2.03, 2.03] 
aor_early_anc4_parity_2_3 
adjusted odds ratio of EANC4+ in women with a parity of 23 
List 
[0.74, 0.74] 
aor_early_anc4_parity_4_5 
adjusted odds ratio of EANC4+ in women with a parity of 45 
List 
[0.65, 0.65] 
aor_early_anc4_parity_6+ 
adjusted odds ratio of EANC4+ in women with a parity of 6+ 
List 
[0.61, 0.61] 
aor_early_anc4_secondary_edu 
adjusted odds ratio of EANC4+ in women with secondary education 
List 
[1.24, 1.24] 
aor_early_anc4_tertiary_edu 
adjusted odds ratio of EANC4+ in women with tertiary education 
List 
[2.64, 2.64] 
aor_early_anc4_richest_wealth 
adjusted odds ratio of EANC4+ in women in the richest wealth quintile 
List 
[1.32, 1.32] 
prob_late_initiation_anc4 
probability a woman will undertake 4 or more ANC visits with the first being after 4 months 
List 
[0.3, 0.29] 
prob_early_initiation_anc_below4 
probabilities a woman will attend fewer than 4 ANC visits but the first visit will occur before month 4 
List 
[0.115, 0.101] 
prob_early_anc_at_facility_level_1_2 
probabilities a woman will attend ANC 1 at facility levels 1 or 2 
List 
[[0.5, 0.5], [0.5, 0.5]] 
treatment_effect_ectopic_pregnancy_treatment 
Treatment effect of ectopic pregnancy case management 
List 
[0.1, 0.1] 
treatment_effect_post_abortion_care 
Treatment effect of post abortion care 
List 
[0.2, 0.2] 
treatment_effect_iron_folic_acid_anaemia 
relative effect of daily iron and folic acid treatment on risk of maternal anaemia 
List 
[0.3, 0.3] 
treatment_effect_calcium_pre_eclamp 
risk reduction of preeclampsia for women taking daily calcium supplementation 
List 
[0.45, 0.45] 
treatment_effect_gest_htn_calcium 
Effect of calcium supplementation on risk of developing gestational hypertension 
List 
[0.65, 0.65] 
treatment_effect_anti_htns_progression 
Effect of anti hypertensive medication in reducing the risk of progression from mild to severe hypertension 
List 
[0.49, 0.49] 
prob_glycaemic_control_diet_exercise 
probability a womans GDM is controlled by diet and exercise during the first month of treatment 
List 
[0.5, 0.5] 
prob_glycaemic_control_orals 
probability a womans GDM is controlled by oral antidiabetics during the first month of treatment 
List 
[0.936, 0.936] 
treatment_effect_gdm_case_management 
Treatment effect of GDM case management on mothers risk of stillbirth 
List 
[0.9, 0.9] 
treatment_effect_still_birth_food_sups 
risk reduction of still birth for women receiving nutritional supplements 
List 
[0.6, 0.6] 
anc_service_structure 
stores type of ANC service being delivered in the model (anc4 or anc8) and is used in analysisscripts to change ANC structure 
Integer 
8 
analysis_year 
Year on which the pregnancy analysis event is scheduled to update any relevant parameters for analysis (1st day 1st month) 
Integer 
2023 
ps_analysis_in_progress 
Used within the pregnancy_helper_function to signify that analysis is currently being conducted 
Boolean 
False 
alternative_anc_coverage 
Signals within the analysis event that an alternative level of ANC coverage has been determined following the events run 
Boolean 
False 
alternative_anc_quality 
Signals within the analysis event that an alternative level of ANC quality has been determined following the events run 
Boolean 
False 
anc_availability_odds 
Target odds of early initiation of ANC4+ when analysis is being conducted  only applied ifalternative_anc_coverage is true 
Real 
9.0 
anc_availability_probability 
Target probability of quality/consumables when analysis is being conducted  only applied if alternative_anc_quality is true 
Real 
0.9 
alternative_ip_anc_quality 
Signals within the analysis event that an alternative level of inpatient ANC quality has been determined following the events run 
Boolean 
False 
ip_anc_availability_probability 
Target probability of quality/consumables when analysis is being conducted  only applied if alternative_ip_anc_quality is true 
Real 
0.9 
sens_analysis_min 
Signals within the analysis event and code that sensitivity analysis is being undertaken in which ANC is blocked from occurring 
Boolean 
False 
sens_analysis_max 
Signals within the analysis event and code that sensitivity analysis is being undertaken in which the maximum coverage of ANC is enforced 
Boolean 
False 
ProstateCancer
Name 
Description 
Type 
Value 

init_prop_prostate_ca_stage 
initial proportions in prostate cancer stages for men aged 3549 
List 
[0.0001, 0.0001, 5e05] 
init_prop_urinary_symptoms_by_stage 
initial proportions of those in prostate ca stages that have urinary symptoms 
List 
[0.3, 0.5, 0.7] 
init_prop_pelvic_pain_symptoms_by_stage 
initial proportions of those in prostate ca stages that have pelvic pain symptoms 
List 
[0.0, 0.3, 0.7] 
init_prop_with_urinary_symptoms_diagnosed_prostate_ca_by_stage 
initial proportions of people with prostate ca and urinary symptoms that have been diagnosed 
List 
[0.3, 0.4, 0.5] 
init_prop_with_pelvic_pain_symptoms_diagnosed_prostate_ca_by_stage 
initial proportions of people with prostate ca and pelvic pain symptoms that have been diagnosed 
List 
[0.3, 0.4, 0.5] 
init_prop_treatment_status_prostate_ca 
initial proportions of people with prostate ca that had received treatment 
List 
[0.1, 0.1, 0.1] 
init_prob_palliative_care 
initial probability of being under palliative care if at metastatic stage 
Real 
0.95 
r_prostate_confined_prostate_ca_none 
probabilty per 3 months of incident (prostate confined) prostate cancer amongst people with no prostate ca (men, age3549) 
Real 
4e05 
rr_prostate_confined_prostate_ca_age5069 
rate ratio for incident (prostate confined) prostate cancer amongst men aged 5069 
Real 
2.0 
rr_prostate_confined_prostate_ca_agege70 
rate ratio for incident (prostate confined) prostate cancer amongst men aged ge 70 
Real 
4.0 
r_local_ln_prostate_ca_prostate_confined 
probabilty per 3 months of local lymph node involved prostate ca amongst people with prostate confined prostate ca 
Real 
0.15 
rr_local_ln_prostate_ca_undergone_curative_treatment 
rate ratio for local lymph node involved prostate ca for people with prostate confined prostate cadue to undergoing curative treatment 
Real 
0.1 
r_metastatic_prostate_ca_local_ln 
probabilty per 3 months of metastatic prostate cancer amongst people with local lymph nodeinvolved prostate ca 
Real 
0.15 
rr_metastatic_prostate_ca_undergone_curative_treatment 
rate ratio for metastatic prostate cancer stage 1 for people with lymph node involved prostate ca due toundergoing curative treatment 
Real 
0.2 
r_death_metastatic_prostate_cancer 
probabilty per 3 months of death from prostate cancer mongst people with metastatic prostate cancer 
Real 
0.2 
r_urinary_symptoms_prostate_ca 
rate of urinary symptoms if have prostate confined prostate ca 
Real 
0.05 
rr_urinary_symptoms_local_ln_or_metastatic_prostate_cancer 
rate ratio of urinary symptoms in a person with local lymph node or metastatuc prostate cancer compared with prostate confined prostate ca 
Real 
1.5 
r_pelvic_pain_symptoms_local_ln_prostate_ca 
rate of pelvic pain or numbness symptoms if have local lymph node involved prostate cancer 
Real 
0.05 
rr_pelvic_pain_metastatic_prostate_cancer 
rate ratio of pelvic pain or numbness in a person with metastatic prostate cancer compared with lymph node involved prostate cancer 
Real 
1.5 
rp_prostate_cancer_age5069 
stagespecific relative prevalence at baseline of prostate cancer for age 5069 
Real 
2.0 
rp_prostate_cancer_agege70 
stagespecific relative prevalence at baseline of prostate cancer for age 70+ 
Real 
4.0 
sensitivity_of_psa_test_for_prostate_ca 
sensitivity of psa test for prostate cancer 
Real 
0.9 
sensitivity_of_biopsy_for_prostate_ca 
sensitivity of biopsy for prostate cancer 
Real 
0.95 
RTI
Name 
Description 
Type 
Value 

base_rate_injrti 
Base rate of RTI per year 
Real 
0.00420322902234662 
rr_injrti_age04 
risk ratio of RTI in age 04 compared to base rate of RTI 
Real 
0.145533 
rr_injrti_age59 
risk ratio of RTI in age 59 compared to base rate of RTI 
Real 
0.551895 
rr_injrti_age1017 
risk ratio of RTI in age 1017 compared to base rate of RTI 
Real 
0.967017 
rr_injrti_age1829 
risk ratio of RTI in age 1829 compared to base rate of RTI 
Real 
1.184184 
rr_injrti_age3039 
risk ratio of RTI in age 3039 compared to base rate of RTI 
Real 
1.052843 
rr_injrti_age4049 
risk ratio of RTI in age 4049 compared to base rate of RTI 
Real 
1.074376 
rr_injrti_age5059 
risk ratio of RTI in age 5059 compared to base rate of RTI 
Real 
1.336449 
rr_injrti_age6069 
risk ratio of RTI in age 6069 compared to base rate of RTI 
Real 
2.308514 
rr_injrti_age7079 
risk ratio of RTI in age 7079 compared to base rate of RTI 
Real 
4.031226 
rr_injrti_male 
risk ratio of RTI when male compared to females 
Real 
2.7 
rr_injrti_excessalcohol 
risk ratio of RTI in those that consume excess alcohol compared to those who do not 
Real 
6.53 
imm_death_proportion_rti 
Proportion of those involved in an RTI that die at site of accident or die before seeking medical intervention 
Real 
0.007 
prob_bleeding_leads_to_shock 
The proportion of those with heavily bleeding injuries who go into shock 
Real 
0.042222 
prob_death_iss_less_than_9 
Proportion of people who pass away in the following month after medical treatment for injuries with an ISSscore less than or equal to 9 
Real 
0.00733191462346883 
prob_death_iss_10_15 
Proportion of people who pass away in the following month after medical treatment for injuries with an ISSscore from 10 to 15 
Real 
0.0111021545889758 
prob_death_iss_16_24 
Proportion of people who pass away in the following month after medical treatment for injuries with an ISSscore from 16 to 24 
Real 
0.0313608577284893 
prob_death_iss_25_35 
Proportion of people who pass away in the following month after medical treatment for injuries with an ISSscore from 25 to 34 
Real 
0.133987145668097 
prob_death_iss_35_plus 
Proportion of people who pass away in the following month after medical treatment for injuries with an ISSscore 35 and above 
Real 
0.22782740761579 
prob_perm_disability_with_treatment_severe_TBI 
probability that someone with a treated severe TBI is permanently disabled 
Real 
0.199 
prob_death_TBI_SCI_no_treatment 
probability that someone with a spinal cord injury will die without treatment 
Real 
0.9 
prop_death_burns_no_treatment 
probability that someone with a burn injury will die without treatment 
Real 
0.6 
prob_death_fractures_no_treatment 
probability that someone with a fracture injury will die without treatment 
Real 
0.1 
prob_TBI_require_craniotomy 
probability that someone with a traumatic brain injury will require a craniotomy surgery 
Real 
0.124 
prob_exploratory_laparotomy 
probability that someone with an internal organ injury will require a exploratory_laparotomy 
Real 
0.319 
prob_depressed_skull_fracture 
Probability that a skull fracture will be depressed and therefore require surgery 
Real 
0.14 
prob_mild_burns 
Probability that a burn within a region will result in < 10% total body surface area 
Real 
0.56 
prob_dislocation_requires_surgery 
Probability that a dislocation will require surgery to relocate the joint. 
Real 
0.01 
number_of_injured_body_regions_distribution 
The distribution of number of injured AIS body regions, used to decide how many injuries a person has 
List 
[[1, 2, 3, 4, 5, 6, 7, 8], [0.7362050184224718, 0.19421990546958515, 0.051237591074077896, 0.013517104401461814, 0.0035659777825202245, 0.0009407486372638106, 0.0002481810186400668, 6.547319397917849e05]] 
injury_location_distribution 
The distribution of where injuries are located in the body, based on the AIS body region definition 
List 
[[1, 2, 3, 4, 5, 6, 7, 8], [0.1438, 0.1325, 0.021, 0.0945, 0.0612, 0.0155, 0.1685, 0.363]] 
mean_los_ISS_less_than_4 
Mean length of stay for someone with an ISS score < 4 
Real 
4.97 
sd_los_ISS_less_than_4 
Standard deviation in length of stay for someone with an ISS score < 4 
Real 
4.86 
mean_los_ISS_4_to_8 
Mean length of stay for someone with an ISS score between 4 and 8 
Real 
8.91 
sd_los_ISS_4_to_8 
Standard deviation in length of stay for someone with an ISS score between 4 and 8 
Real 
5.93 
mean_los_ISS_9_to_15 
Mean length of stay for someone with an ISS score between 9 and 15 
Real 
15.46 
sd_los_ISS_9_to_15 
Standard deviation in length of stay for someone with an ISS score between 9 and 15 
Real 
11.16 
mean_los_ISS_16_to_24 
Mean length of stay for someone with an ISS score between 16 and 24 
Real 
24.73 
sd_los_ISS_16_to_24 
Standard deviation in length of stay for someone with an ISS score between 16 and 24 
Real 
17.03 
mean_los_ISS_more_than_25 
Mean length of stay for someone with an ISS score between 16 and 24 
Real 
30.86 
sd_los_ISS_more_that_25 
Standard deviation in length of stay for someone with an ISS score between 16 and 24 
Real 
34.03 
daly_wt_unspecified_skull_fracture 
daly_wt_unspecified_skull_fracture  code 1674 
Real 
0.195 
daly_wt_basilar_skull_fracture 
daly_wt_basilar_skull_fracture  code 1675 
Real 
0.149 
daly_wt_epidural_hematoma 
daly_wt_epidural_hematoma  code 1676 
Real 
0.185 
daly_wt_subdural_hematoma 
daly_wt_subdural_hematoma  code 1677 
Real 
0.21 
daly_wt_subarachnoid_hematoma 
daly_wt_subarachnoid_hematoma  code 1678 
Real 
0.214 
daly_wt_brain_contusion 
daly_wt_brain_contusion  code 1679 
Real 
0.174 
daly_wt_intraventricular_haemorrhage 
daly_wt_intraventricular_haemorrhage  code 1680 
Real 
0.174 
daly_wt_diffuse_axonal_injury 
daly_wt_diffuse_axonal_injury  code 1681 
Real 
0.239 
daly_wt_subgaleal_hematoma 
daly_wt_subgaleal_hematoma  code 1682 
Real 
0.174 
daly_wt_midline_shift 
daly_wt_midline_shift  code 1683 
Real 
0.239 
daly_wt_facial_fracture 
daly_wt_facial_fracture  code 1684 
Real 
0.067 
daly_wt_facial_soft_tissue_injury 
daly_wt_facial_soft_tissue_injury  code 1685 
Real 
0.008 
daly_wt_eye_injury 
daly_wt_eye_injury  code 1686 
Real 
0.054 
daly_wt_neck_soft_tissue_injury 
daly_wt_neck_soft_tissue_injury  code 1687 
Real 
0.1 
daly_wt_neck_internal_bleeding 
daly_wt_neck_internal_bleeding  code 1688 
Real 
0.1 
daly_wt_neck_dislocation 
daly_wt_neck_dislocation  code 1689 
Real 
0.187 
daly_wt_chest_wall_bruises_hematoma 
daly_wt_chest_wall_bruises_hematoma  code 1690 
Real 
0.143 
daly_wt_hemothorax 
daly_wt_hemothorax  code 1691 
Real 
0.143 
daly_wt_lung_contusion 
daly_wt_lung_contusion  code 1692 
Real 
0.205 
daly_wt_diaphragm_rupture 
daly_wt_diaphragm_rupture  code 1693 
Real 
0.205 
daly_wt_rib_fracture 
daly_wt_rib_fracture  code 1694 
Real 
0.187 
daly_wt_flail_chest 
daly_wt_flail_chest  code 1695 
Real 
0.211 
daly_wt_chest_wall_laceration 
daly_wt_chest_wall_laceration  code 1696 
Real 
0.143 
daly_wt_closed_pneumothorax 
daly_wt_closed_pneumothorax  code 1697 
Real 
0.164 
daly_wt_open_pneumothorax 
daly_wt_open_pneumothorax  code 1698 
Real 
0.164 
daly_wt_surgical_emphysema 
daly_wt_surgical_emphysema aka subcuteal emphysema  code 1699 
Real 
0.164 
daly_wt_abd_internal_organ_injury 
daly_wt_abd_internal_organ_injury  code 1700 
Real 
0.182 
daly_wt_spinal_cord_lesion_neck_with_treatment 
daly_wt_spinal_cord_lesion_neck_with_treatment  code 1701 
Real 
0.589 
daly_wt_spinal_cord_lesion_neck_without_treatment 
daly_wt_spinal_cord_lesion_neck_without_treatment  code 1702 
Real 
0.732 
daly_wt_spinal_cord_lesion_below_neck_with_treatment 
daly_wt_spinal_cord_lesion_below_neck_with_treatment  code 1703 
Real 
0.296 
daly_wt_spinal_cord_lesion_below_neck_without_treatment 
daly_wt_spinal_cord_lesion_below_neck_without_treatment  code 1704 
Real 
0.623 
daly_wt_vertebrae_fracture 
daly_wt_vertebrae_fracture  code 1705 
Real 
0.111 
daly_wt_clavicle_scapula_humerus_fracture 
daly_wt_clavicle_scapula_humerus_fracture  code 1706 
Real 
0.035 
daly_wt_hand_wrist_fracture_with_treatment 
daly_wt_hand_wrist_fracture_with_treatment  code 1707 
Real 
0.01 
daly_wt_hand_wrist_fracture_without_treatment 
daly_wt_hand_wrist_fracture_without_treatment  code 1708 
Real 
0.014 
daly_wt_radius_ulna_fracture_short_term_with_without_treatment 
daly_wt_radius_ulna_fracture_short_term_with_without_treatment  code 1709 
Real 
0.028 
daly_wt_radius_ulna_fracture_long_term_without_treatment 
daly_wt_radius_ulna_fracture_long_term_without_treatment  code 1710 
Real 
0.043 
daly_wt_dislocated_shoulder 
daly_wt_dislocated_shoulder  code 1711 
Real 
0.062 
daly_wt_amputated_finger 
daly_wt_amputated_finger  code 1712 
Real 
0.005 
daly_wt_amputated_thumb 
daly_wt_amputated_thumb  code 1713 
Real 
0.011 
daly_wt_unilateral_arm_amputation_with_treatment 
daly_wt_unilateral_arm_amputation_with_treatment  code 1714 
Real 
0.039 
daly_wt_unilateral_arm_amputation_without_treatment 
daly_wt_unilateral_arm_amputation_without_treatment  code 1715 
Real 
0.118 
daly_wt_bilateral_arm_amputation_with_treatment 
daly_wt_bilateral_arm_amputation_with_treatment  code 1716 
Real 
0.123 
daly_wt_bilateral_arm_amputation_without_treatment 
daly_wt_bilateral_arm_amputation_without_treatment  code 1717 
Real 
0.383 
daly_wt_foot_fracture_short_term_with_without_treatment 
daly_wt_foot_fracture_short_term_with_without_treatment  code 1718 
Real 
0.026 
daly_wt_foot_fracture_long_term_without_treatment 
daly_wt_foot_fracture_long_term_without_treatment  code 1719 
Real 
0.026 
daly_wt_patella_tibia_fibula_fracture_with_treatment 
daly_wt_patella_tibia_fibula_fracture_with_treatment  code 1720 
Real 
0.05 
daly_wt_patella_tibia_fibula_fracture_without_treatment 
daly_wt_patella_tibia_fibula_fracture_without_treatment  code 1721 
Real 
0.055 
daly_wt_hip_fracture_short_term_with_without_treatment 
daly_wt_hip_fracture_short_term_with_without_treatment  code 1722 
Real 
0.258 
daly_wt_hip_fracture_long_term_with_treatment 
daly_wt_hip_fracture_long_term_with_treatment  code 1723 
Real 
0.058 
daly_wt_hip_fracture_long_term_without_treatment 
daly_wt_hip_fracture_long_term_without_treatment  code 1724 
Real 
0.402 
daly_wt_pelvis_fracture_short_term 
daly_wt_pelvis_fracture_short_term  code 1725 
Real 
0.279 
daly_wt_pelvis_fracture_long_term 
daly_wt_pelvis_fracture_long_term  code 1726 
Real 
0.182 
daly_wt_femur_fracture_short_term 
daly_wt_femur_fracture_short_term  code 1727 
Real 
0.111 
daly_wt_femur_fracture_long_term_without_treatment 
daly_wt_femur_fracture_long_term_without_treatment  code 1728 
Real 
0.042 
daly_wt_dislocated_hip 
daly_wt_dislocated_hip  code 1729 
Real 
0.016 
daly_wt_dislocated_knee 
daly_wt_dislocated_knee  code 1730 
Real 
0.113 
daly_wt_amputated_toes 
daly_wt_amputated_toes  code 1731 
Real 
0.006 
daly_wt_unilateral_lower_limb_amputation_with_treatment 
daly_wt_unilateral_lower_limb_amputation_with_treatment  code 1732 
Real 
0.039 
daly_wt_unilateral_lower_limb_amputation_without_treatment 
daly_wt_unilateral_lower_limb_amputation_without_treatment  code 1733 
Real 
0.173 
daly_wt_bilateral_lower_limb_amputation_with_treatment 
daly_wt_bilateral_lower_limb_amputation_with_treatment  code 1734 
Real 
0.088 
daly_wt_bilateral_lower_limb_amputation_without_treatment 
daly_wt_bilateral_lower_limb_amputation_without_treatment  code 1735 
Real 
0.443 
rt_emergency_care_ISS_score_cut_off 
A parameter to determine which level of injury severity corresponds to the emergency health care seeking symptom and which to the nonemergency generic injury symptom 
Integer 
5 
prob_death_MAIS3 
A parameter to determine the probability of death without medical intervention with a military AISscore of 3 
Real 
0.05 
prob_death_MAIS4 
A parameter to determine the probability of death without medical intervention with a military AISscore of 4 
Real 
0.31 
prob_death_MAIS5 
A parameter to determine the probability of death without medical intervention with a military AISscore of 5 
Real 
0.59 
prob_death_MAIS6 
A parameter to determine the probability of death without medical intervention with a military AISscore of 6 
Real 
0.83 
femur_fracture_skeletal_traction_mean_los 
The mean length of stay for a person with a femur fracture being treated with skeletal traction 
Integer 
52 
other_skeletal_traction_los 
The mean length of stay for a person with a nonfemur fracture being treated with skeletal traction 
Integer 
42 
prob_foot_frac_require_cast 
The probability that a person with a foot fracture will be treated with a plaster cast 
Real 
0.613 
prob_foot_frac_require_maj_surg 
The probability that a person with a foot fracture will be treated with a major surgery 
Real 
0.263 
prob_foot_frac_require_min_surg 
The probability that a person with a foot fracture will be treated with a major surgery 
Real 
0.038 
prob_foot_frac_require_amp 
The probability that a person with a foot fracture will be treated with amputation via a major surgery 
Real 
0.086 
prob_tib_fib_frac_require_cast 
The probability that a person with a tibia/fibula fracture will be treated with a plaster cast 
Real 
0.71 
prob_tib_fib_frac_require_maj_surg 
The probability that a person with a tibia/fibula fracture will be treated with a major surgery 
Real 
0.066 
prob_tib_fib_frac_require_min_surg 
The probability that a person with a tibia/fibula fracture will be treated with a minor surgery 
Real 
0.175 
prob_tib_fib_frac_require_amp 
The probability that a person with a tibia/fibula fracture will be treated with an amputation via major surgery 
Real 
0.024 
prob_tib_fib_frac_require_traction 
The probability that a person with a tibia/fibula fracture will be treated with skeletal traction 
Real 
0.025 
prob_femural_fracture_require_major_surgery 
The probability that a person with a femur fracture will be treated with major surgery 
Real 
0.187 
prob_femural_fracture_require_minor_surgery 
The probability that a person with a femur fracture will be treated with minor surgery 
Real 
0.007 
prob_femural_fracture_require_cast 
The probability that a person with a femur fracture will be treated with a plaster cast 
Real 
0.024 
prob_femural_fracture_require_amputation 
The probability that a person with a femur fracture will be treated with amputation via major surgery 
Real 
0.005 
prob_femural_fracture_require_traction 
The probability that a person with a femur fracture will be treated with skeletal traction 
Real 
0.777 
prob_pelvis_fracture_traction 
The probability that a person with a pelvis fracture will be treated with skeletal traction 
Real 
0.71 
prob_pelvis_frac_major_surgery 
The probability that a person with a pelvis fracture will be treated with major surgery 
Real 
0.12 
prob_pelvis_frac_minor_surgery 
The probability that a person with a pelvis fracture will be treated with minor surgery 
Real 
0.05 
prob_pelvis_frac_cast 
The probability that a person with a pelvis fracture will be treated with a cast 
Real 
0.12 
prob_dis_hip_require_maj_surg 
The probability that a person with a dislocated hip will be treated with a major surgery 
Real 
0.167 
prob_dis_hip_require_cast 
The probability that a person with a dislocated hip will be treated with a plaster cast 
Real 
0.333 
prob_hip_dis_require_traction 
The probability that a person with a dislocated hip will be treated with skeletal traction 
Real 
0.5 
hdu_cut_off_iss_score 
The ISS score used as a criteria to admit patients to the HDU/ICU units 
Integer 
29 
mean_icu_days 
The mean length of stay in the ICUfor those without TBI 
Real 
4.8 
sd_icu_days 
The standard deviation in length of stay in the ICU for those without TBI 
Real 
6.0 
mean_tbi_icu_days 
The mean length of stay in the ICU for those with TBI 
Real 
8.4 
sd_tbi_icu_days 
The standard deviation in length of stay in the ICU for those with TBI 
Real 
6.4 
prob_open_fracture_contaminated 
The probability that an open fracture will be contaminated 
Real 
0.07 
allowed_interventions 
List of additional interventions that can be included when performing model analysis 
List 
[] 
head_prob_112 
The probability that this person’s head injury is a skull fracture 
Real 
0.0455 
head_prob_113 
The probability that this person’s head injury is a basilar skull fracture 
Real 
0.0045 
head_prob_133a 
The probability that this person’s head injury is a Subarachnoid hematoma 
Real 
0.09149906 
head_prob_133b 
The probability that this person’s head injury is a Brain contusion 
Real 
0.301946898 
head_prob_133c 
The probability that this person’s head injury is an Intraventricular haemorrhage 
Real 
0.013724859 
head_prob_133d 
The probability that this person’s head injury is a Subgaleal hematoma 
Real 
0.050324483 
head_prob_134a 
The probability that this person’s head injury is an Epidural hematoma 
Real 
0.086670324 
head_prob_134b 
The probability that this person’s head injury is a Subdural hematoma 
Real 
0.080003376 
head_prob_135 
The probability that this person’s head injury is a Diffuse axonal injury/midline shift 
Real 
0.061731 
head_prob_1101 
The probability that this person’s head injury is a laceration 
Real 
0.253536 
head_prob_1114 
The probability that this person’s head injury is a burn 
Real 
0.010564 
face_prob_211 
The probability that this person’s face injury is a Facial fracture (nasal/unspecified) 
Real 
0.158585 
face_prob_212 
The probability that this person’s face injury is a Facial fracture (mandible/zygomatic) 
Real 
0.294515 
face_prob_241 
The probability that this person’s face injury is a soft tissue injury 
Real 
0.339 
face_prob_2101 
The probability that this person’s face injury is a laceration 
Real 
0.194845 
face_prob_2114 
The probability that this person’s face injury is a burn 
Real 
0.010255 
face_prob_291 
The probability that this person’s face injury is an eye injury 
Real 
0.0028 
neck_prob_3101 
The probability that this person’s neck injury is a laceration 
Real 
0.06972 
neck_prob_3113 
The probability that this person’s neck injury is a burn 
Real 
0.01428 
neck_prob_342 
The probability that this person’s neck injury is a Soft tissue injury in neck (vertebral artery laceration) 
Real 
0.004 
neck_prob_343 
The probability that this person’s neck injury is a Soft tissue injury in neck (pharynx contusion) 
Real 
0.004 
neck_prob_361 
The probability that this person’s neck injury is a Sternomastoid m. hemorrhage/ Hemorrhage, supraclavicular triangle/Hemorrhage, posterior triangle/Anterior vertebral vessel hemorrhage/ Neck muscle hemorrhage 
Real 
0.495 
neck_prob_363 
The probability that this person’s neck injury is a Hematoma in carotid sheath/Carotid sheath hemorrhage 
Real 
0.405 
neck_prob_322 
The probability that this person’s neck injury is an Atlantooccipital subluxation 
Real 
0.00264 
neck_prob_323 
The probability that this person’s neck injury is an Atlantoaxial subluxation 
Real 
0.00536 
thorax_prob_4101 
The probability that this person’s thorax injury is a laceration 
Real 
0.49036 
thorax_prob_4113 
The probability that this person’s thorax injury is a burn 
Real 
0.04264 
thorax_prob_461 
The probability that this person’s thorax injury is Chest wall bruises/haematoma 
Real 
0.0945 
thorax_prob_463 
The probability that this person’s thorax injury is Haemothorax 
Real 
0.0945 
thorax_prob_453a 
The probability that this person’s thorax injury is a Lung contusion 
Real 
0.0539 
thorax_prob_453b 
The probability that this person’s thorax injury is a Diaphragm rupture 
Real 
0.0161 
thorax_prob_412 
The probability that this person’s thorax injury is a rib fracture 
Real 
0.0392 
thorax_prob_414 
The probability that this person’s thorax injury is flail chest 
Real 
0.0098 
thorax_prob_441 
The probability that this person’s thorax injury is a Chest wall lacerations/avulsions 
Real 
0.08586 
thorax_prob_442 
The probability that this person’s thorax injury is a Surgical emphysema 
Real 
0.01749 
thorax_prob_443 
The probability that this person’s thorax injury is a Closed pneumothorax/ open pneumothorax 
Real 
0.05565 
abdomen_prob_5101 
The probability that this person’s abdomen injury is a laceration 
Real 
0.11026 
abdomen_prob_5113 
The probability that this person’s thorax injury is a burn 
Real 
0.03874 
abdomen_prob_552 
The probability that this person’s thorax injury is a skull fracture 
Real 
0.047656 
abdomen_prob_553 
The probability that this person’s thorax injury is an Injury to stomach/intestines/colon 
Real 
0.77441 
abdomen_prob_554 
The probability that this person’s thorax injury is an Injury to spleen/Urinary bladder/Liver/Urethra/Diaphragm 
Real 
0.028934 
spine_prob_612 
The probability that this person’s spine injury is a vertabrae fracture 
Real 
0.364 
spine_prob_673a 
The probability that this person’s spine injury is a Spinal cord injury at neck level 
Real 
0.015840216 
spine_prob_673b 
The probability that this person’s spine injury is a Spinal cord injury below neck level 
Real 
0.040731984 
spine_prob_674a 
The probability that this person’s spine injury is a Spinal cord injury at neck level 
Real 
0.074477731 
spine_prob_674b 
The probability that this person’s spine injury is a Spinal cord injury below neck level 
Real 
0.116490809 
spine_prob_675a 
The probability that this person’s spine injury is a Spinal cord injury at neck level 
Real 
0.134791137 
spine_prob_675b 
The probability that this person’s spine injury is a Spinal cord injury below neck level 
Real 
0.210827163 
spine_prob_676 
The probability that this person’s spine injury is a Spinal cord injury at neck level 
Real 
0.04284096 
upper_ex_prob_7101 
The probability that this person’s upper extremity injury is a laceration 
Real 
0.43896 
upper_ex_prob_7113 
The probability that this person’s upper extremity injury is a burn 
Real 
0.03304 
upper_ex_prob_712a 
The probability that this person’s upper extremity injury is a Fracture to Clavicle, scapula, humerus 
Real 
0.10802 
upper_ex_prob_712b 
The probability that this person’s upper extremity injury is a Fracture to Hand/wrist 
Real 
0.28969 
upper_ex_prob_712c 
The probability that this person’s upper extremity injury is a Fracture to Radius/ulna 
Real 
0.09329 
upper_ex_prob_722 
The probability that this person’s upper extremity injury is a dislocated shoulder 
Real 
0.025 
upper_ex_prob_782a 
The probability that this person’s upper extremity injury is an Amputated finger 
Real 
0.00750024 
upper_ex_prob_782b 
The probability that this person’s upper extremity injury is a Unilateral arm amputation 
Real 
0.00102276 
upper_ex_prob_782c 
The probability that this person’s upper extremity injury is a Thumb amputation 
Real 
0.002841 
upper_ex_prob_783 
The probability that this person’s upper extremity injury is a bilateral arm amputation 
Real 
0.000636 
lower_ex_prob_8101 
The probability that this person’s lower extremity injury is a laceration 
Real 
0.186094109 
lower_ex_prob_8113 
The probability that this person’s lower extremity injury is a burn 
Real 
0.014007083 
lower_ex_prob_811 
The probability that this person’s lower extremity injury is a foot fracture 
Real 
0.023610948 
lower_ex_prob_813do 
The probability that this person’s lower extremity injury is an open foot fracture 
Real 
0.013281158 
lower_ex_prob_812 
The probability that this person’s lower extremity injury is a Fracture to patella, tibia, fibula, ankle 
Real 
0.354164215 
lower_ex_prob_813eo 
The probability that this person’s lower extremity injury is an open Fracture to patella, tibia, fibula, ankle 
Real 
0.199217371 
lower_ex_prob_813a 
The probability that this person’s lower extremity injury is a Hip fracture 
Real 
0.029513685 
lower_ex_prob_813b 
The probability that this person’s lower extremity injury is a Pelvis fracture 
Real 
0.023610948 
lower_ex_prob_813bo 
The probability that this person’s lower extremity injury is an open Pelvis fracture 
Real 
0.005902737 
lower_ex_prob_813c 
The probability that this person’s lower extremity injury is a Femur fracture 
Real 
0.076765094 
lower_ex_prob_813co 
The probability that this person’s lower extremity injury is an open Femur fracture 
Real 
0.01177596 
lower_ex_prob_822a 
The probability that this person’s lower extremity injury is a Dislocated hip 
Real 
0.037338982 
lower_ex_prob_822b 
The probability that this person’s lower extremity injury is a Dislocated knee 
Real 
0.002383339 
lower_ex_prob_882 
The probability that this person’s lower extremity injury is an Amputation of toes 
Real 
0.00731139 
lower_ex_prob_883 
The probability that this person’s lower extremity injury is a Unilateral leg amputation 
Real 
0.007511491 
lower_ex_prob_884 
The probability that this person’s lower extremity injury is a Bilateral leg amputation 
Real 
0.007511491 
blocked_interventions 
A list of interventions that are blocked in a simulation 
List 
[] 
unavailable_treatment_mortality_mais_cutoff 
A cutoff score above which an injury will result in additional mortality if the person has sought healthcare and not received it. 
Integer 
5 
consider_death_no_treatment_ISS_cut_off 
A cutoff score above which an injuries will be considered severe enough to cause mortality in those whohave not sought care. 
Integer 
15 
maximum_number_of_times_HSI_events_should_run 
limit on the number of times an HSI event can run 
Integer 
5 
Schisto
Name 
Description 
Type 
Value 

prob_sent_to_lab_test_children 
Probability that infected child gets sent to lab test 
Real 
0.9 
prob_sent_to_lab_test_adults 
Probability that an infected adults gets sent to lab test 
Real 
0.6 
delay_till_hsi_a_repeated 
Time till seeking healthcare again after not being sent to schisto test: start 
Real 
5.0 
delay_till_hsi_b_repeated 
Time till seeking healthcare again after not being sent to schisto test: end 
Real 
20.0 
PZQ_efficacy 
The efficacy of Praziquantel in clearing burden of any Schistosomiasis worm species 
Real 
1.0 
MDA_coverage_historical 
Probability of getting PZQ in the MDA for PSAC, SAC and Adults in historic rounds 
Dataframe 

MDA_coverage_prognosed 
Probability of getting PZQ in the MDA for PSAC, SAC and Adults in future rounds, with the frequency given in months 
Dataframe 

sm_beta_PSAC 
Contact/exposure rate of PSAC 
Real 
0.3 
sm_beta_SAC 
Contact/exposure rate of SAC 
Real 
1.0 
sm_beta_Adults 
Contact/exposure rate of Adults 
Real 
0.05 
sm_worms_fecundity 
Fecundity parameter, driving densitydependent reproduction 
Real 
0.0006 
sm_worm_lifespan 
Lifespan of the worm in human host given in years 
Real 
4.0 
sm_high_intensity_threshold 
Threshold of worm burden indicating high intensity infection 
Real 
46.0 
sm_low_intensity_threshold 
Threshold of worm burden indicating low intensity infection 
Real 
2.0 
sm_high_intensity_threshold_PSAC 
Worm burden threshold for high intensity infection in PSAC 
Real 
20.0 
sm_reservoir_2010 
Initial reservoir of infectious material per district in 2010 
Series 

sm_gamma_alpha 
Parameter alpha for Gamma distribution for harbouring rates 
Series 

sm_R0 
Effective reproduction number, for the FOI 
Series 

sh_beta_PSAC 
Contact/exposure rate of PSAC 
Real 
0.3 
sh_beta_SAC 
Contact/exposure rate of SAC 
Real 
1.0 
sh_beta_Adults 
Contact/exposure rate of Adults 
Real 
0.05 
sh_worms_fecundity 
Fecundity parameter, driving densitydependent reproduction 
Real 
0.005 
sh_worm_lifespan 
Lifespan of the worm in human host given in years 
Real 
6.0 
sh_high_intensity_threshold 
Threshold of worm burden indicating high intensity infection 
Real 
20.0 
sh_low_intensity_threshold 
Threshold of worm burden indicating low intensity infection 
Real 
2.0 
sh_high_intensity_threshold_PSAC 
Worm burden threshold for high intensity infection in PSAC 
Real 
5.0 
sh_reservoir_2010 
Initial reservoir of infectious material per district in 2010 
Series 

sh_gamma_alpha 
Parameter alpha for Gamma distribution for harbouring rates 
Series 

sh_R0 
Effective reproduction number, for the FOI 
Series 
MDA_coverage_historical
PSAC 
SAC 
Adults 

0 
0.85 
0.44 
0 
0.92 
0.88 
0 
0.87 
0.88 
0 
0.73 
0.02 
0 
0.8 
0.155 
0 
0.87 
0.29 
0 
0.87 
0.9 
0 
0.48 
0.96 
0 
0.605 
0.96 
Only first 10 rows of 128 are shown.
MDA_coverage_prognosed
PSAC 
SAC 
Adults 

0.5 
0.8 
0.5 
0.5 
0.8 
0.5 
0.5 
0.8 
0.5 
0.5 
0.8 
0.5 
0.5 
0.8 
0.5 
0 
0.8 
0.5 
0 
0.8 
0.5 
0 
0.8 
0.5 
0 
0.8 
0.5 
Only first 10 rows of 32 are shown.
sm_reservoir_2010
Reservoir 

0.0796066 
0.0796066 
0.0243277 
0.158777 
0 
0 
0 
0.0891927 
0 
Only first 10 rows of 32 are shown.
sm_gamma_alpha
alpha_value 

0.0652093 
0.0652093 
0.056 
0.07445 
0.05 
0.05 
0.05 
0.0665 
0.05 
Only first 10 rows of 32 are shown.
sm_R0
R0_value 

1.46175 
1.46175 
2.18968 
1.26817 
0 
0 
0 
1.42196 
0 
Only first 10 rows of 32 are shown.
sh_reservoir_2010
Reservoir 

1.87216 
0 
0 
2.81222 
0 
0 
0 
0 
0 
Only first 10 rows of 32 are shown.
sh_gamma_alpha
alpha_value 

0.107616 
0.04664 
0.0805 
0.1377 
0.08905 
0.0698 
0 
0.0643 
0.0793714 
Only first 10 rows of 32 are shown.
sh_R0
R0_value 

1.12956 
1.1253 
1.1248 
1.14141 
1.12577 
1.12423 
0 
1.12421 
1.12471 
Only first 10 rows of 32 are shown.
Stunting
Name 
Description 
Type 
Value 

prev_HAZ_distribution_age_0_5mo 
Distribution of HAZ among less than 6 months of age in 2015 (mean, standard deviation) 
List 
[0.8482365, 1.416337] 
prev_HAZ_distribution_age_6_11mo 
Distribution of HAZ among 6 months and 1 year of age in 2015 (mean, standard deviation) 
List 
[0.9940219, 1.504431] 
prev_HAZ_distribution_age_12_23mo 
Distribution of HAZ among 1 year olds in 2015 (mean, standard deviation) 
List 
[1.522101, 1.431207] 
prev_HAZ_distribution_age_24_35mo 
Distribution of HAZ among 2 year olds in 2015 (mean, standard deviation) 
List 
[1.669291, 1.343577] 
prev_HAZ_distribution_age_36_47mo 
Distribution of HAZ among 3 year olds in 2015 (mean, standard deviation) 
List 
[1.797365, 1.212469] 
prev_HAZ_distribution_age_48_59mo 
Distribution of HAZ among 4 year olds in 2015 (mean, standard deviation) 
List 
[1.620094, 1.11541] 
or_stunting_male 
Odds ratio of stunting if male gender 
Real 
1.38 
or_stunting_preterm_and_AGA 
Odds ratio of stunting if born preterm and adequate for gestational age 
Real 
2.13 
or_stunting_SGA_and_term 
Odds ratio of stunting if born term and small for geatational age 
Real 
2.36 
or_stunting_SGA_and_preterm 
Odds ratio of stunting if born preterm and small for gestational age 
Real 
5.95 
or_stunting_hhwealth_Q5 
Odds ratio of stunting if household wealth is poorest Q5, ref group Q1 
Real 
1.69 
or_stunting_hhwealth_Q4 
Odds ratio of stunting if household wealth is poorer Q4, ref group Q1 
Real 
1.48 
or_stunting_hhwealth_Q3 
Odds ratio of stunting if household wealth is middle Q3, ref group Q1 
Real 
1.4 
or_stunting_hhwealth_Q2 
Odds ratio of stunting if household wealth is richer Q2, ref group Q1 
Real 
1.29 
base_inc_rate_stunting_by_agegp 
Baseline incidence rate per year of stunting by age group (15, 611, 1223, 2435, 3647, 4859mo 
List 
[0.8, 0.8, 0.8, 0.8, 0.8, 0.8] 
rr_stunting_preterm_and_AGA 
Relative risk of stunting if born preterm and adequate for gestational age 
Real 
1.62 
rr_stunting_SGA_and_term 
Relative risk of stunting if born term and small for gestational age 
Real 
1.65 
rr_stunting_SGA_and_preterm 
Relative risk of stunting if born preterm and small for gestational age 
Real 
2.98 
rr_stunting_prior_wasting 
Relative risk of stunting if prior wasting in the last 3 months 
Real 
1.93 
rr_stunting_untreated_HIV 
Relative risk of stunting for untreated HIV+ 
Real 
1.5 
rr_stunting_wealth_level 
Relative risk of stunting if wealthlevel is greater than 1 compared 1 
Real 
0.2 
rr_stunting_no_exclusive_breastfeeding 
Relative risk of stunting for not exclusively breastfed babies < 6 months 
Real 
1.4 
rr_stunting_no_continued_breastfeeding 
Relative risk of stunting for not continued breastfed infants 624 months 
Real 
1.3 
rr_stunting_per_diarrhoeal_episode 
Relative risk of stunting for recent diarrhoea episode 
Real 
1.04 
r_progression_severe_stunting_by_agegp 
Rates per year of progression to severe stunting by age group (15, 611, 1223, 2435, 3647, 4859mo 
List 
[0.8, 0.8, 0.8, 0.8, 0.8, 0.8] 
rr_progress_severe_stunting_if_prior_wasting 
Relative risk of severe stunting if previously wasted 
Real 
1.93 
rr_progress_severe_stunting_untreated_HIV 
Relative risk of severe stunting for untreated HIV+ 
Real 
1.3 
mean_years_to_1stdev_natural_improvement_in_stunting 
Mean time (in years) to a one standard deviation improvement in stunting without any treatment. 
Real 
1.840675229013975 
effectiveness_of_complementary_feeding_education_in_stunting_reduction 
Probability of stunting being reduced by one standard deviation (category) by education about supplementary feeding (but not supplying supplementary feeding consmables). 
Real 
0.25 
effectiveness_of_food_supplementation_in_stunting_reduction 
Probability of stunting being reduced by one standard deviation (category) by supplementary feeding. 
Real 
0.41 
prob_stunting_diagnosed_at_generic_appt 
Probability of a stunted or severely stunted person being checked and correctly diagnosed 
Real 
0.01 
SymptomManager
Name 
Description 
Type 
Value 

generic_symptoms_spurious_occurrence 
probability and duration of spurious occureneces of generic symptoms 
Dataframe 

spurious_symptoms 
whether or not there will be the spontaneous occurrence of generic symptoms. NB. This is overridden if a module keyword argument is provided. 
Boolean 
True 
generic_symptoms_spurious_occurrence
name 
odds_ratio_health_seeking_in_children 
odds_ratio_health_seeking_in_adults 
prob_spurious_occurrence_in_children_per_day 
prob_spurious_occurrence_in_adults_per_day 
duration_in_days_of_spurious_occurrence_in_children 
duration_in_days_of_spurious_occurrence_in_adults 
prob_seeks_emergency_appt_in_adults 
prob_seeks_emergency_appt_in_children 

vomiting 
1.31 
0.48 
0.001 
0.001 
7 
4 
0 
0 
stomachache 
0.7 
0.48 
0.001 
0.001 
7 
4 
0 
0 
sore_throat 
1.07 
0.58 
0.001 
0.001 
7 
4 
0 
0 
respiratory_symptoms 
0.55 
0.48 
0.001 
0.001 
7 
4 
0 
0 
headache 
0.39 
0.28 
0.001 
0.001 
7 
4 
0 
0 
skin_complaint 
2.82 
0.76 
0.001 
0.001 
7 
4 
0 
0 
dental_complaint 
0.39 
0.92 
0.001 
0.001 
7 
4 
0 
0 
backache 
1 
0.56 
0.001 
0.001 
7 
4 
0 
0 
injury 
0.55 
0.68 
0.001 
0.001 
7 
4 
0 
0 
Only first 10 rows of 13 are shown.
Tb
Name 
Description 
Type 
Value 

prop_mdr2010 
Proportion of active tb cases with multidrug resistance in 2010 
Real 
0.0186 
followup_times 
times(weeks) tb treatment monitoring required after tx start 
Dataframe 

tb_high_risk_distr 
list of ten highrisk districts 
Dataframe 

ipt_coverage 
national estimates of coverage of IPT in PLHIV and paediatric contacts 
Dataframe 

rr_tb_child 
relative risk of tb infection if under 16 years of age 
Real 
0.1 
monthly_prob_relapse_tx_complete 
monthly probability of relapse once treatment complete 
Real 
0.0027 
monthly_prob_relapse_tx_incomplete 
monthly probability of relapse if treatment incomplete 
Real 
0.0116 
monthly_prob_relapse_2yrs 
monthly probability of relapse 2 years after treatment complete 
Real 
0.0001 
rr_relapse_hiv 
relative risk of relapse for HIVpositive people 
Real 
4.7 
rr_relapse_diabetes 
relative risk of relapse for people with diabetes (treated/untreated) 
Real 
1.86 
scaling_factor_WHO 
scaling factor applied to WHO estimates to account for the impact of interventions in place 
Real 
1.60303 
duration_active_disease_years 
duration of active disease from onset to cure or death 
Real 
3.0 
prop_smear_positive 
proportion of new active cases that will be smearpositive 
Real 
0.62 
prop_smear_positive_hiv 
proportion of hiv+ active tb cases that will be smearpositive 
Real 
0.35 
death_rate_smear_pos_untreated 
probability of death in smearpositive tb cases with untreated tb 
Real 
0.7 
death_rate_smear_neg_untreated 
probability of death in smearnegative tb cases with untreated tb 
Real 
0.2 
death_rate_child0_4_treated 
probability of death in child aged 04 years with treated tb 
Real 
0.05 
death_rate_child5_14_treated 
probability of death in child aged 514 years with treated tb 
Real 
0.06 
death_rate_adult_treated 
probability of death in adult aged >=15 years with treated tb 
Real 
0.107 
rr_death_diabetes 
additional risk of death if person has diabetes (treated/untreated) 
Real 
1.51 
rr_tb_bcg 
relative risk of progression to active disease for children with BCG vaccine 
Real 
0.42 
rr_tb_hiv 
relative risk of progression to active disease for PLHIV 
Real 
5.0 
rr_tb_aids 
relative risk of progression to active disease for PLHIV with AIDS 
Real 
26.0 
rr_tb_art_adult 
relative risk of progression to active disease for adults with HIV on ART 
Real 
0.35 
rr_tb_art_child 
relative risk of progression to active disease for adults with HIV on ART 
Real 
0.3 
rr_tb_obese 
relative risk of progression to active disease if obese 
Real 
0.4 
rr_tb_diabetes 
relative risk of progression to active disease with any type diabetes 
Real 
3.0 
rr_tb_alcohol 
relative risk of progression to active disease with heavy alcohol use 
Real 
2.9 
rr_tb_smoking 
relative risk of progression to active disease with smoking 
Real 
1.3 
rr_ipt_adult 
relative risk of active TB with IPT in adults 
Real 
0.4 
rr_ipt_child 
relative risk of active TB with IPT in children 
Real 
0.55 
rr_ipt_adult_hiv 
relative risk of active TB with IPT in adults with hiv 
Real 
0.68 
rr_ipt_child_hiv 
relative risk of active TB with IPT in children with hiv 
Real 
0.31 
rr_ipt_art_adult 
relative risk of active TB with IPT and ART in adults 
Real 
0.63 
rr_ipt_art_child 
relative risk of active TB with IPT and ART in children 
Real 
0.76 
sens_xpert_smear_negative 
sensitivity of Xpert test in smear negative TB cases 
Real 
0.68 
sens_xpert_smear_positive 
sensitivity of Xpert test in smear positive TB cases 
Real 
0.98 
spec_xpert_smear_negative 
specificity of Xpert test in smear negative TB cases 
Real 
0.99 
spec_xpert_smear_positive 
specificity of Xpert test in smear positive TB cases 
Real 
0.99 
sens_sputum_smear_positive 
sensitivity of sputum smear microscopy in sputum positive cases 
Real 
1.0 
spec_sputum_smear_positive 
specificity of sputum smear microscopy in sputum positive cases 
Real 
1.0 
sens_clinical 
sensitivity of clinical diagnosis in detecting active TB 
Real 
0.209 
spec_clinical 
specificity of clinical diagnosis in detecting TB 
Real 
0.953 
sens_xray_smear_negative 
sensitivity of xray diagnosis in smear negative TB cases 
Real 
0.8 
sens_xray_smear_positive 
sensitivity of xray diagnosis in smear positive TB cases 
Real 
0.91 
spec_xray_smear_negative 
specificity of xray diagnosis in smear negative TB cases 
Real 
0.67 
spec_xray_smear_positive 
specificity of xray diagnosis in smear positive TB cases 
Real 
0.67 
prob_tx_success_ds 
Probability of treatment success for new and relapse TB cases 
Real 
0.837 
prob_tx_success_mdr 
Probability of treatment success for MDRTB cases 
Real 
0.597 
prob_tx_success_0_4 
Probability of treatment success for children aged 04 years 
Real 
0.94 
prob_tx_success_5_14 
Probability of treatment success for children aged 514 years 
Real 
0.92 
rate_testing_general_pop 
rate of screening / testing per month in general population 
Real 
0.025 
rate_testing_active_tb 
rate of screening / testing per month in population with active tb 
Dataframe 

ds_treatment_length 
length of treatment for drugsusceptible tb (first case) in months 
Real 
6.0 
ds_retreatment_length 
length of treatment for drugsusceptible tb (secondary case) in months 
Real 
8.0 
mdr_treatment_length 
length of treatment for mdrtb in months 
Real 
24.0 
prob_retained_ipt_6_months 
probability of being retained on IPT every 6 months if still eligible 
Real 
0.9 
age_eligibility_for_ipt 
eligibility criteria (years of age) for IPT given to contacts of TB cases 
Real 
5.0 
ipt_start_date 
year from which IPT is available for paediatric contacts of diagnosed active TB cases 
Integer 
2014 
first_line_test 
name of first test to be used for TB diagnosis 
String 
sputum 
second_line_test 
name of second test to be used for TB diagnosis 
String 
xpert 
tb_healthseekingbehaviour_cap 
number of repeat visits assumed for healthcare services 
Integer 
5 
data_end 
last year for which data are available 
Integer 
2022 
length_of_inpatient_stay_if_terminal 
length of inpatient stay for endoflife TB patients 
List 
[5, 10] 
type_of_scaleup 
argument to determine type scaleup of program which will be implemented, can be ‘none’, ‘target’ or ‘max’ 
String 
none 
scaleup_start_year 
the year when the scaleup starts (it will occur on 1st January of that year) 
Integer 
2025 
scaleup_parameters 
the parameters and values changed in scenario analysis 
Dataframe 
followup_times
ds_sputum 
ds_clinical_monitor 
ds_retreatment_sputum 
ds_retreatment_clinical 
mdr_sputum 
mdr_clinical_monitor 
shine_sputum 
shine_clinical_monitor 

5 
2 
5 
2 
5 
2 
4 
2 
6 
3 
8 
3 
6 
3 
nan 
3 
nan 
4 
nan 
4 
8 
4 
nan 
4 
nan 
5 
nan 
5 
10 
5 
nan 
nan 
nan 
6 
nan 
6 
12 
6 
nan 
nan 
nan 
nan 
nan 
7 
14 
7 
nan 
nan 
nan 
nan 
nan 
8 
16 
8 
nan 
nan 
nan 
nan 
nan 
nan 
18 
9 
nan 
nan 
nan 
nan 
nan 
nan 
20 
10 
nan 
nan 
Only first 10 rows of 24 are shown.
tb_high_risk_distr
district_name 

Blantyre 
Blantyre City 
Chikwawa 
Chiradzulu 
Chitipa 
Dedza 
Dowa 
Karonga 
Kasungu 
Only first 10 rows of 32 are shown.
ipt_coverage
year 
coverage_plhiv 
source 
coverage_paediatric 
source2 

2011 
0 
not_implemented 
0 
nan 
2012 
0 
not_implemented 
0 
nan 
2013 
0 
not_implemented 
0 
nan 
2014 
0 
not_implemented 
35 
NTP2019 
2015 
0 
not_implemented 
42 
NTP2019 
2016 
0 
not_implemented 
51 
NTP2019 
2017 
0 
not_implemented 
61 
NTP2019 
2018 
0.31 
MoH_quart_repQ1 
57 
NTP2019 
2019 
0.3 
MoH_quart_repQ2 
57 
NTP2020 
Only first 10 rows of 41 are shown.
rate_testing_active_tb
year 
case_notification_rate_per_100k 
treatment_coverage 
treatment_success_rates 
death_rate 
percent_hiv_positive 
number_notified_mdr_cases 
percent_mdr_treatment_success 
percent_death_mdr_cases 
coverage_ipt_paediatric_contacts 

2011 
nan 
46 
82.7 
10.7 
nan 
nan 
nan 
nan 
nan 
2012 
138 
51 
81.8 
10.7 
nan 
27 
63.2 
31.6 
nan 
2013 
126 
48 
83.3 
9.8 
nan 
91 
52.6 
36.8 
nan 
2014 
112 
46 
85 
8.9 
nan 
106 
58.6 
34 
35 
2015 
105 
46 
81.6 
10.6 
42.6 
107 
60.9 
32.8 
42 
2016 
101 
47 
82.1 
10.3 
38.8 
66 
58.6 
29.3 
51 
2017 
95 
50 
86 
9.7 
39.1 
85 
55 
35 
61 
2018 
88 
48 
87.2 
8.6 
38.5 
126 
68.8 
17 
57 
2019 
92 
51 
87.6 
8.2 
35.5 
104 
73 
16 
57 
Only first 10 rows of 12 are shown.
scaleup_parameters
parameter 
target_value 
min_value 
max_value 

tb_treatment_coverage 
90 
0 
100 
tb_prob_tx_success_ds 
0.9 
0 
1 
tb_prob_tx_success_mdr 
0.9 
0 
1 
tb_prob_tx_success_0_4 
0.9 
0 
1 
tb_prob_tx_success_5_14 
0.9 
0 
1 
first_line_test 
xpert 
sputum 
xpert 
second_line_test 
sputum 
sputum 
xpert 
ipt_coverage_plhiv 
0.9 
0 
1 
ipt_coverage_paediatric 
90 
0 
100 